DISCOVERY PARTNERS INTERNATIONAL INC - 10-Q Quarterly Report

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-Q

QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

SECURITIES EXCHANGE ACT OF 1934

For the Quarterly Period Ended June 30, 2004

Commission File Number 000-31141

DISCOVERY PARTNERS

INTERNATIONAL, INC.

(Exact Name of registrant as specified in its charter)

Delaware	33-0655706
(State or other jurisdiction of	(I.R.S. employer identification number)
incorporation or organization)

9640 Towne Centre Drive
San Diego, California 92121	(858) 455-8600
(Address of principal executive	(Registrant’s telephone number,
offices and zip code)	Including area code)

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.

Yes ý No o

Indicate by check mark whether the Registrant is an accelerated filer (as defined in Exchange Act Rule 12b-2).

Yes ý No o

As of August 3, 2004 a total of 26,074,151 shares of the Registrant’s Common Stock, $0.001 par value, were issued and outstanding.

DISCOVERY PARTNERS INTERNATIONAL, INC.

FORM 10-Q

TABLE OF CONTENTS

PART I.	FINANCIAL INFORMATION
Item 1.	Financial Statements:
	Condensed Consolidated Balance Sheets At June 30, 2004 (unaudited) and December 31, 2003
	Condensed Consolidated Statements of Operations for the Three and Six Months Ended June 30, 2004 and 2003 (unaudited)
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2004 and 2003 (unaudited)
	Notes to Consolidated Financial Statements
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations
Item 3.	Quantitative and Qualitative Disclosures About Market Risk
Item 4.	Controls and Procedures
PART II.	OTHER INFORMATION
Item 1.	Legal Proceedings
Item 2.	Changes in Securities, Use of Proceeds and Issuer Purchases of Equity Securities
Item 3.	Defaults Upon Senior Securities
Item 4.	Submission of Matters to a Vote of Security Holders
Item 5.	Other Information
Item 6.	Exhibits and Reports on Form 8-K

DISCOVERY PARTNERS INTERNATIONAL, INC.

PART I

FINANCIAL INFORMATION

Item 1. Financial Statements

Discovery Partners International, Inc.

Condensed Consolidated Balance Sheets

	June 30, 2004			December 31, 2003
	(unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	6,783,232		$	7,846,026
Short-term investments	71,072,601			64,728,243
Accounts receivable, net	12,319,724			11,874,784
Inventories, net	4,427,511			4,148,230
Prepaid and other current assets	1,896,831			1,583,262
Total current assets	96,499,899			90,180,545
Restricted cash	1,046,508			1,196,672
Property and equipment, net	7,802,127			8,408,028
Prepaid royalty, net	5,431,179			6,034,643
Patent and license rights, net	2,453,845			2,620,839
Other assets, net	601,580			743,275
Total assets	$	113,835,138		$	109,184,002
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable and accrued expenses	$	2,628,684		$	1,880,553
Accrued compensation	2,024,296			3,908,475
Restructuring accrual	535,501			744,141
Deferred revenue	3,436,007			4,305,936
Total current liabilities	8,624,488			10,839,105
Deferred rent	134,125			97,964
Stockholders’ equity:
Preferred stock, $.001 par value, 1,000,000 shares authorized, no shares issued and outstanding at June 30, 2004 and December 31, 2003	—			—
Common stock, $.001 par value, 100,000,000 shares authorized, 25,966,497 and 24,744,831 issued and outstanding at June 30, 2004 and December 31, 2003, respectively	25,966			24,745
Common stock issuable	1,026,000			1,026,000
Treasury stock, at cost, 216,886 shares at June 30, 2004 and December 31, 2003	(775,459		)	(775,451		)
Additional paid-in capital	207,090,354			201,685,793
Deferred compensation	(707,215		)	(1,054,797		)
Accumulated other comprehensive income	262,437			971,970
Accumulated deficit	(101,845,558		)	(103,631,327		)
Total stockholders’ equity	105,076,525			98,246,933
Total liabilities and stockholders’ equity	$	113,835,138		$	109,184,002

See accompanying notes

Discovery Partners International, Inc.

Condensed Consolidated Statements of Operations

(Unaudited)

	Three Months Ended							Six Months Ended
	June 30, 2004				June 30, 2003			June 30, 2004				June 30, 2003
Revenues:
Services	$	11,699,274			$	10,768,053		$		21,973,539		$	22,733,628
Products	1,299,891				480,068			2,832,977				1,217,713
Total revenues	12,999,165				11,248,121			24,806,516				23,951,341
Cost of revenues:
Services	7,063,248				6,664,852			12,726,791				15,129,610
Products	743,854				591,955			1,631,145				1,233,999
Total cost of revenues	7,807,102				7,256,807			14,357,936				16,363,609
Gross margin	5,192,063				3,991,314			10,448,580				7,587,732
Operating expenses:
Research and development	899,694				662,953			1,793,118				1,367,161
Selling, general and administrative	3,596,485				3,399,586			7,158,760				6,473,082
Restructuring	—				1,557,562			—				1,557,562
Amortization of stock-based compensation	134,544				75,326			304,382				159,954
Total operating expenses	4,630,723				5,695,427			9,256,260				9,557,759
Income (loss) from operations	561,340				(1,704,113		)	1,192,320				(1,970,027			)
Interest income, net	295,580				447,793			633,408				993,083
Foreign currency transaction gains (losses), net	(96,940			)	(4,756		)	(48,537			)	(6,625			)
Other income (expense), net	(19,725			)	—			8,578				—
Net income (loss)	$		740,255		$	(1,261,076	)	$	1,785,769			$		(983,569	)
Net income (loss) per share, basic	$		0.03		$	(0.05	)	$	0.07			$		(0.04	)
Weighted average shares outstanding, basic	25,168,680				24,297,508			24,851,022				24,310,262
Net income (loss) per share, diluted	$		0.03		$	(0.05	)	$	0.07			$		(0.04	)
Weighted average shares outstanding, diluted	26,031,368				24,297,508			25,877,632				24,310,262

The composition of stock-based compensation is as follows:
Cost of revenues	$		45		$	846		$	233			$		2,084
Research and development	675				31,073			6,153				71,590
Selling, general and administrative	133,824				43,407			297,996				86,280
	$		134,544		$	75,326		$	304,382			$		159,954

See accompanying notes

Discovery Partners International, Inc.

Condensed Consolidated Statements of Cash Flows

(Unaudited)

	Six Months Ended
	June 30, 2004			June 30, 2003

OPERATING ACTIVITIES
Net income (loss)	$	1,785,769		$	(983,569	)
Adjustments to reconcile net income (loss) to cash provided by operating activities:
Depreciation and amortization	2,778,985			2,496,986
Amortization of stock-based compensation	318,929			159,954
Restructuring expense	—			1,557,562
Realized (gain) loss on investments	102,619			(24,518		)
Change in operating assets and liabilities:
Accounts receivable	(493,823		)	58,074
Inventories	(380,364		)	1,595,827
Other current assets	(318,379		)	246,946
Accounts payable and accrued expenses	(1,461,013		)	167,084
Restructuring accrual	(208,640		)	(303,268		)
Contract loss accrual	—			(837,522		)
Deferred revenue	(806,924		)	659,032
Deferred rent	36,161			(720		)
Restricted cash	150,164			(1,081		)
Net cash provided by operating activities	1,503,484			4,790,787
INVESTING ACTIVITIES
Purchases of property and equipment	(950,240		)	(798,542		)
Other assets	44,248			200,953
Purchase of patents, license rights and prepaid royalties	(65,465		)	(2,092,194		)
Proceeds from sales and maturity of short-term investments	23,842,133			30,171,190
Purchases of short-term investments	(30,875,502		)	(34,913,881		)
Net cash used in investing activities	(8,004,826		)	(7,432,474		)
FINANCING ACTIVITIES
Principal payments on capital leases and line of credit, net	—			(447,971		)
Net proceeds from issuance of common stock	5,434,427			226,707
Purchase of treasury stock	—			(289,000		)
Net cash provided by (used in) financing activities	5,434,427			(510,264		)
Effect of exchange rate changes	4,121			(290,583		)
Net decrease in cash and cash equivalents	(1,062,794		)	(3,442,534		)
Cash and cash equivalents at beginning of period	7,846,026			8,309,269
Cash and cash equivalents at end of period	$	6,783,232		$	4,866,735
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION
Interest paid	$	29,291		$	90,321
NON-CASH INVESTING AND FINANCING ACTIVITIES:
Unrealized loss on investments	$	303,623		$	581,238

See accompanying notes

DISCOVERY PARTNERS INTERNATIONAL, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

JUNE 30, 2004

1. Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and disclosures required by accounting principles generally accepted in the United States for complete financial statements. The condensed consolidated balance sheet as of June 30, 2004, condensed consolidated statements of operations for the three and six months ended June 30, 2004 and 2003, and the condensed consolidated statements of cash flows for the six months ended June 30, 2004 and 2003 are unaudited, but include all adjustments (consisting of normal recurring adjustments), which Discovery Partners International, Inc. (the Company) considers necessary for a fair presentation of the financial position, results of operations and cash flows for the periods presented. The results of operations for the three and six months ended June 30, 2004 shown herein are not necessarily indicative of the results that may be expected for the year ending December 31, 2004. For more complete financial information, these financial statements, and notes thereto, should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2003 included in the Company’s Form 10-K filed with the Securities and Exchange Commission.

The consolidated financial statements include all of the accounts of the Company and its wholly owned subsidiaries, Discovery Partners International AG (DPI AG), ChemRx Advanced Technologies, Inc., Xenometrix, Inc., Structural Proteomics, Inc., Discovery Partners International L.L.C. (DPI LLC), Systems Integration Drug Discovery Company, Inc. (substantially inactive) and Irori Europe, Ltd. (substantially inactive). All intercompany accounts and transactions have been eliminated.

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, such as, inventory, intangible assets and restructuring accruals, at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

2. Net Income Per Share

Basic and diluted net income per share is presented in conformity with Statement of Financial Accounting Standard (SFAS) No. 128, Earnings per Share. In accordance with SFAS No. 128, basic net income per share has been computed by dividing net income by the weighted average number of shares of common stock outstanding during the period, less shares subject to repurchase. Diluted net income per share has been computed by dividing net income by the weighted-average number of common shares outstanding and common stock equivalent shares outstanding during the period calculated using the treasury stock method, less shares subject to repurchase. Common stock equivalent shares, composed of outstanding stock options and warrants, are included in diluted net income per share to the extent these shares are dilutive. The computations for basic and diluted earnings per share are as follows:

	Income (Numerator)		Shares (Denominator)	Earnings Per Share
Three Months Ended June 30, 2004
Basic earnings per share:
Net income	$	740,255	25,168,680	$	0.03
Diluted earnings per share:
Dilutive stock options	—		620,188	—
Contingently issuable restricted stock	—		242,500	—
Net income plus assumed conversions	$	740,255	26,031,368	$	0.03

Six Months Ended June 30, 2004
Basic earnings per share:
Net income	$	1,785,769	24,851,022	$	0.07
Diluted earnings per share:
Dilutive stock options	—		784,110	—
Common stock issuable	—		242,500	—
Net income plus assumed conversions	$	1,785,769	25,877,632	$	0.07

The computations for basic and diluted earnings per share for the three and six months ended June 2003 are not shown herein as all common stock equivalent shares were antidilutive. The total number of shares issuable upon exercise of stock options and warrants excluded from the calculation of diluted earnings per share since they are anti-dilutive were 1,964,656 and 1,367,336 for the three and six months ended June 30, 2004, respectively, and 2,582,550 and 2,700,924 for the three and six months ended June 30, 2004.

In July 2004, 400,000 restricted stock grants were awarded pursuant to the Company’s 2000 Stock Incentive Plan to certain of the Company’s key employees. The issuance of these shares would not have changed the results of earnings per share if the shares were outstanding during the three and six months ended June 30, 2004.

3. Stock-Based Compensation

As permitted by SFAS No. 123, Accounting for Stock-Based Compensation, as amended by SFAS No. 148, Accounting for Stock-Based Compensation---Transition and Disclosure, the Company accounts for common stock options granted to employees and directors using the intrinsic value method and, thus, recognizes no compensation expense for such stock-based awards where the exercise prices are equal to or greater than the fair value of the Company’s common stock on the date of the grant. Pro forma information regarding net income or loss is required by SFAS No. 123 and SFAS No. 148, and has been determined as if the Company had accounted for its employee stock options under the fair value method of SFAS No. 123. The fair value of these options was estimated at the date of grant using the Black-Scholes option pricing model with the following weighted average assumptions used for option grants:

	Three and Six Months Ended June 30,
	2004		2003
Risk-free interest rate	3.5	%	4.5	%
Dividend yield	0	%	0	%
Volatility factor	87	%	97	%
Weighted average life in years	6.7		6.6

For purposes of adjusted pro forma disclosures, the estimated fair value of the options is amortized to expense over the vesting period. The Company’s adjusted pro forma information is as follows:

	Three Months Ended							Six Months Ended
	June 30, 2004				June 30, 2003			June 30, 2004				June 30, 2003
Net Income (loss), as reported	$	740,255			$	(1,261,076	)	$		1,785,769		$	(983,569		)
Deduct: Total stock-based compensation expense determined under fair value based method	(725,558			)	(755,063		)	(1,451,864			)	(1,540,527			)
Pro forma net income (loss)	$		14,697		$	(2,016,139	)	$	333,905			$	(2,524,096		)

Earnings (loss) per share:
Basic and diluted — as reported	$		0.03		$	(0.05	)	$		0.07		$		(0.04	)
Basic and diluted — pro forma	$		0.00		$	(0.08	)	$		0.01		$		(0.10	)

4. Comprehensive Income (Loss)

SFAS No. 130, Reporting Comprehensive Income, requires the Company to report, in addition to net income (loss), comprehensive income (loss) and its components. A summary follows:

	Three Months Ended								Six Months Ended
	June 30, 2004				June 30, 2003				June 30, 2004			June 30, 2003

Comprehensive income (loss):
Foreign currency translation adjustment	$		(52,908	)	$		12,541		$	405,910		$	92,914
Unrealized gain (loss) on investments	287,787				(97,868			)	303,623			(314,149			)
Net income (loss).	740,255				(1,261,076			)	1,785,769			(983,569			)
Comprehensive income (loss)	$	975,134			$	(1,346,403		)	$		2,495,302	$		(1,204,804	)

5. Inventory

Inventories are recorded at the lower of weighted average cost or market. Inventories consist of the following:

	June 30, 2004				December 31, 2003
Raw materials	$	1,493,749			$	1,712,503
Work-in-process	3,957,997				3,555,779
Finished goods	17,544,350				17,961,132
	22,996,096				23,229,414
Less reserves	(18,568,585			)	(19,081,184		)
	$		4,427,511		$	4,148,230

6. Prepaid Royalty, Patents and License Rights

Prepaid royalty, patents and license rights consist of the following:

	June 30, 2004							December 31, 2003
	Gross Carrying Value		Accumulated Amortization			Net		Gross Carrying Value		Accumulated Amortization			Net
Prepaid royalty	$	6,034,643	$	(603,464	)	$	5,431,179	$	6,034,643	$			$	6,034,643
Patents	2,832,620		(824,608		)	2,008,012		2,765,804		(685,945		)	2,079,859
License rights	1,256,667		(810,834		)	445,833		1,585,862		(1,044,882		)	540,980
Other intangible assets			—			—		1,221,105		(1,221,105		)	—

Total intangible assets	$	10,123,930	$	(2,238,906	)	$	7,885,024	$	10,386,309	$	(1,730,827	)	$		8,655,482

Amortization expense related to intangible assets was $397,478 and $837,274 for the three and six months ended June 30, 2004, respectively and $187,509 and $379,912 for the three and six months ended June 30, 2003, respectively. The Company began amortization in 2004 of the prepaid royalty of $6,034,643 for royalties the Company prepaid to Abbott Laboratories related to the µARCS screening technology. This amortization is being recorded ratably over five years. The estimated amortization expense of intangible assets for the second half of fiscal 2004 is approximately $794,422 and for each of the five succeeding years ending December 31 is as shown in the following table. Actual amortization expense to be reported in future periods could differ from these estimates as a result of acquisitions, divestitures, asset impairments and other factors.


2005	$		1,588,845
2006	1,588,845
2007	1,588,845
2008	1,584,678
2009	739,390
Thereafter	—
	$	7,090,603

7. Deferred Stock Compensation

In conjunction with the Company’s initial public offering completed in July 2000, the Company recorded deferred stock compensation totaling approximately $2.7 million and $1.0 million during the years ended December 31, 2000 and 1999, respectively, representing the difference at the date of grant between the exercise or purchase price and estimated fair value of the Company’s common stock as estimated by the Company’s management. Additionally, in August 2003, awards of 52,500 shares and rights to acquire 190,000 shares of restricted stock were awarded pursuant to the Company’s 2000 Stock Incentive Plan to certain of the Company’s key employees resulting in an increase in deferred compensation of $1.3 million. The restricted stock and rights to acquire restricted stock vest in annual installments over a four-year period. In accordance with APB No. 25, deferred compensation is included as a reduction of stockholders’ equity and is being amortized to expense on an accelerated basis in accordance with Financial Accounting Standards Board Interpretation No. 28 over the vesting period of the options, restricted stock and rights to acquire restricted stock. During the three and six months ended June 30, 2004 and 2003, the Company recorded amortization of stock-based compensation expense of $134,544 and $304,382, and $75,326 and $159,954 respectively.

8. Restructuring Accrual

In April 2003, the Company announced that it would consolidate its domestic chemistry facilities into two centers of excellence: in South San Francisco for primary screening library design and synthesis programs and in San Diego for lead optimization and medicinal chemistry projects. At the same time, the Company announced its plans to establish new offshore chemistry capabilities to take advantage of lower cost structures. These actions resulted in the closure of its Tucson facility. In accordance with SFAS No. 146, Accounting for Costs Associated with Exit or Disposal Activities, severance and retention bonuses for involuntary employee terminations and the costs to exit certain contractual and lease obligations were accrued as of the restructuring date. Moving, relocation and other costs related to consolidation of facilities were expensed as incurred. Under the restructuring plan 28 employees were involuntarily terminated, including scientific and administrative staff. Restructuring charges totaled $1,872,986 for the year ended December 31, 2003 and were comprised of the following:


Severance and Retention Bonuses for Involuntary Employee Terminations		$375,599
Costs to Exit Certain Contractual and Lease Obligations		919,171
Moving, Relocation and Other Costs Related to Consolidation of Facilities		578,216
Total Restructuring Expense		$1,872,986

There were no additional costs incurred in the three months ended June 30, 2004.

The following table summarizes the activity and balances of the restructuring reserve:

	Severance and Retention Bonuses for Involuntary Employee Terminations			Costs to Exit Certain Contractual and Lease Obligations			Moving, Relocation and Other Costs Related to Consolidation of Facilities			Total
Balance at December 31, 2002	$	—		$	—		$	—		$		—
Reserve Established	375,599			919,171			578,216			1,872,986
Utilization of reserve:
Payments	(375,599		)	(175,030		)	(578,216		)	(1,128,845			)
Balance at December 31, 2003	$	—		$	744,141		$	—		$	744,141
Utilization of reserve:
Payments	—			(208,640		)	—			(208,640			)
Balance at June 30, 2004	$	—		$	535,501		$	—		$	535,501

The Company expects to complete the utilization of the reserve related to this restructuring by July 2005.

9. Revenues by Product Category

The Company operates in one industry segment: the development, manufacture and marketing of products and services to make the drug discovery process more efficient, less expensive and more likely to generate a drug target. Such products and services include libraries of drug-like compounds, proprietary instruments, consumable supplies, drug discovery services, computational tools to generate compound libraries, and testing and screening services to optimize potential drugs. Additionally, the Company licenses proprietary gene profiling systems. Our products and services are complementary, and share the same customers, distribution and marketing strategies. In addition, in making operating and strategic decisions, the Company’s management evaluates revenues based on the worldwide revenues of each major product line and type of service, and profitability on an enterprise-wide basis. Revenue by product and service category is as follows:

	Three Months Ended					Six Months Ended
	June 30, 2004		June 30, 2003			June 30, 2004			June 30, 2003

Chemistry services	$	9,245,522	$		8,521,955	$	16,635,308		$	18,331,737
Screening services	2,218,576		1,561,016			4,257,750			2,875,117
Products	1,299,891		480,068			2,832,977			1,217,713
Other licenses and services	235,176		685,082			1,080,481			1,526,774
Total revenues	$	12,999,165	$	11,248,121		$		24,806,516	$		23,951,341

A total of 58% and 54% for the three and six months ended June 30, 2004, respectively and 64% and 59% for the three and six months ended June 30, 2003, respectively, of revenue came from the Company’s chemistry contracts with Pfizer.

10. Significant Events

In May 2004, the Company completed a secondary public offering of 8,305,300 shares of common stock at a price of $5.00 per share. Axys Pharmaceuticals, Inc., a stockholder of Discovery Partners, sold 7,222,000 shares. The Company issued the remaining 1,083,300 shares to the underwriters to cover over-allotments. The Company received net proceeds from the offering of $5.1 million.

11. Subsequent Events

In July 2004, 400,000 restricted stock grants were awarded pursuant to the Company’s 2000 Stock Incentive Plan to certain of the Company’s key employees. The restricted stock vests five years from grant date, with accelerated vesting upon achievement of specified Company stock price targets. Compensation expense of $2,104,000 relating to this restricted stock grant will be recognized on an accelerated basis in accordance with Financial Accounting Standards Board Interpretation No. 28 over four years.

DISCOVERY PARTNERS INTERNATIONAL, INC.

PART I

FINANCIAL INFORMATION (continued)

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

THIS FORM 10-Q CONTAINS CERTAIN STATEMENTS THAT ARE NOT STRICTLY HISTORICAL AND ARE “FORWARD-LOOKING” STATEMENTS WITHIN THE MEANING OF THE PRIVATE SECURITIES LITIGATION REFORM ACT OF 1995 AND INVOLVE A HIGH DEGREE OF RISK AND UNCERTAINTY. SUCH STATEMENTS INCLUDE BUT ARE NOT LIMITED TO STATEMENTS REGARDING OUR ESTIMATED FUTURE AMORTIZATION EXPENSE, EXPECTED FUTURE REVENUES UNDER OUR CHEMISTRY CONTRACT WITH PFIZER, THE ESTIMATED COSTS TO CLOSE OUR TUCSON FACILITY, OUR EXPECTED DEFERRED COMPENSATION EXPENSE FOR 2004, OUR CASH RESOURCES, OUR FUTURE CASH FLOWS, OUR FUTURE CAPITAL EXPENDITURES, OUR FUTURE DEBT LEVELS AND STATEMENTS ABOUT OUR EXPECTATIONS RELATED TO PROFITABILITY. OUR ACTUAL RESULTS MAY DIFFER MATERIALLY FROM THOSE PROJECTED IN THE FORWARD-LOOKING STATEMENTS DUE TO RISKS AND UNCERTAINTIES THAT EXIST IN OUR OPERATIONS, DEVELOPMENT EFFORTS AND BUSINESS ENVIRONMENT, INCLUDING THOSE DESCRIBED BELOW UNDER THE HEADING “RISKS AND UNCERTAINTIES” AND THOSE DESCRIBED IN OUR FORM 10-K FOR THE YEAR ENDED DECEMBER 31, 2003 AND OTHER REPORTS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION.

Web Site Access to SEC Filings

We maintain an Internet website at www.discoverypartners.com. We make available free of charge on our Internet website our annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K, and amendments to those reports filed or furnished pursuant to Section 13(a) or 15(d) of the Exchange Act as soon as reasonably practicable after we electronically file such material with, or furnish it to, the SEC.

Overview

We were founded in 1995 as IRORI. In October 1998, we changed our name to Discovery Partners International, Inc. and in July 2000 we completed our initial public offering and simultaneously reincorporated in the state of Delaware.

We sell a broad range of products and services to pharmaceutical and biopharmaceutical companies to make the drug discovery process for our customers faster, less expensive and more effective at generating drug candidates. We focus on the portion of the drug discovery process that begins after identification of a drug target through when a drug candidate is ready for pre-clinical studies. Our major products and services are as follows:

• We develop, produce and sell collections of chemical compounds that pharmaceutical and biopharmaceutical companies test for their potential use as new drugs or for use as the chemical starting point for new drugs.

• We develop, manufacture and sell proprietary instruments and the associated line of consumable supplies that are used by the pharmaceutical and biopharmaceutical industries in their own in-house drug discovery chemistry operations.

• We provide testing services to our customers in which chemical compounds are tested for their biological activity as potential drugs.

• We provide computational software tools that guide the entire process of chemical compound design, development and testing.

• We license our proprietary gene profiling system that characterizes a cell’s response upon exposure to compounds and other agents by the pattern of gene expression in the cell.

We have made a number of acquisitions in recent years that have significantly expanded our overall size and have allowed us to offer customers this broad range of integrated drug discovery products and services from a single provider:

• In December 1999, we acquired Discovery Technologies, Ltd. (now known as Discovery Partners International AG) to provide assay development and high throughput screening services. This addition enabled us to offer screening services together with compounds.

• In April 2000, we acquired Axys Advanced Technologies, for a total consideration of 7,429,641 shares of our common stock and $600,000. This acquisition enabled us to offer the development and production of large compound libraries.

• In May 2000, we acquired 75% of the outstanding shares of Structural Proteomics. This acquisition provided us with computational software and services. At the end of 2002 we acquired all of the remaining shares of Structural Proteomics.

• In January 2001, we acquired Systems Integration Drug Discovery Company, or SIDDCO, enhancing our capabilities in combinatorial chemistry research and development.

• In May 2001, we acquired Xenometrix, Inc. This acquisition provided us with rights to a proprietary gene profiling system that we offer and license and enabled us to offer toxicology research products and services.

The pharmaceutical and biopharmaceutical industries provide substantially all of our revenues.

In the first half of 2004, 54% of our revenue came from our chemistry contract with Pfizer, and we anticipate that this contract will continue to provide for a significant percentage of our revenue throughout 2004 and 2005.

Critical Accounting Policies

This discussion and analysis of our financial condition and results of operations is based upon our financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses. On an ongoing basis, we evaluate our estimates. We base our estimates on historical experience and on various other assumptions that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates, and the estimates themselves might be different if we used different assumptions.

We believe the following critical accounting policies involve significant judgments and estimates that are used in the preparation of our financial statements.

Revenue recognition. Revenue is recognized as follows:

Product sales. Revenue from product sales, which include the sale of instruments and related consumables, is recorded as products are shipped if the costs of such shipments can be reasonably estimated and if all the customer’s acceptance criteria have been met. Certain of our contracts for product sales include customer acceptance provisions that give our customers the right of replacement if the delivered product does not meet specified criteria; however, we have historically demonstrated that the products meet the specified criteria and the number of customers exercising their right of replacement has been insignificant and therefore, once we have completed our internal testing, we recognize revenue without providing for such contingency upon shipment.

Chemistry services. Revenue from the sale of chemical compounds delivered under our chemistry collaborations is recorded as the compounds are shipped. Revenue under chemistry service agreements that are compensated on a full-time equivalent, or FTE, basis is recognized on a monthly basis and is based upon the number of FTE employees that actually worked on each project and the agreed-upon rate per FTE per month. Beginning in April 2004, in accordance with our agreement with Pfizer, we are compensated based on predetermined limits to reserve sufficient resources to complete specific compound related activities, at the customer’s request, whether or not utilized. Revenue for reserving these resources is recognized based on the predetermined limits stipulated in the contract.

Screening services. High throughput screening service revenues are recognized on a percentage-of-completion basis. Advances received under these high throughput screening service agreements are initially recorded as deferred revenue, which is then recognized as costs are incurred over the term of the contract. Certain of these contracts may allow the customer the right to reject the work performed; however, we have no material history of such rejections and historically we have been able to recognize revenue without providing for such contingency.

Other licenses and services. Other licenses and services revenue includes royalty revenue due to us under the Xenometrix patent licensing agreements, development contract revenue, product related services revenue and warranty services revenue related to our instrumentation sales. Royalty revenue is recognized upon receipt of monies, provided we have no future obligation with respect to such payments. Development contract revenues are recognized on a percentage-of-completion basis. Product related service revenues are recognized when the performance of the service is complete. Warranty services revenue is recognized when the related product is shipped and extended warranty services revenue is recognized ratably over the service period.

Integrated drug discovery collaborations may provide chemistry services revenue, screening services revenue and milestone payments and other revenues. Revenue for each of these elements of such collaborations is recognized as described above. Revenue from milestone payments would be recognized upon receipt of monies.

From time to time we receive requests from customers to bill and hold goods for them. In these cases, as long as the specific revenue recognition criteria under accounting principles generally accepted in the United States at the time of the bill and hold are met, including the customer accepting the risk of loss and the transfer of ownership of such goods occurring prior to shipment, the revenue is recognized.

In February 2003, we entered into an agreement with GlaxoSmithKline, or GSK. In accordance with the agreement, we agreed to develop and supply to GSK two complete X-Kan Chemistry Synthesis Systems. X-Kans are chemical microreactors that combine the two-dimensional tagging features of the previously introduced NanoKan technology with an increased size and scale that are similar to the currently available MicroKan and MiniKan products. Revenue under this agreement is recognized on a percentage-of-completion basis, up to contractual limits and is included in other licenses and services revenue. We completed this project in the first half of 2004.

In July 2003, we entered into an agreement with Bruker AXS Inc. Under the terms of the agreement, we appointed Bruker AXS the worldwide distributor for our Crystal Farm line of protein crystallography products. In accordance with SFAS No. 48, Revenue Recognition When Right of Return Exists, and due to the limited sales history we have with this product line, we defer the recognition of revenue until either Bruker AXS receives final acceptance

or payment from the ultimate customer, or we receive final acceptance or payment from Bruker AXS. Revenue from these sales is included in product sales.

Inventory. Inventories are recorded at the lower of cost or market. We write-down our inventory for estimated obsolescence or non-marketability if there is an excess of cost of inventory over the estimated market value based upon assumptions about future demand and market conditions. If actual market conditions are less favorable than we have projected, additional inventory write-downs may be required. As of June 30, 2004, 95% of our inventory reserve is associated with our chemical compound finished goods inventory. A significant portion of our net inventory balance represents work-in-process related to two multi-year chemistry collaborations. Estimated losses on any deliverables are recorded when they become apparent. As of June 30, 2004, we have reserved approximately $262,000 against the work-in-process representing the anticipated losses on the sale of chemical compound libraries.

Long-lived assets. In accounting for long-lived assets, we make estimates about the expected useful lives and the potential for impairment. Changes in the marketplace, technology or our operations could result in changes to these estimates. Our long-lived assets are evaluated for impairment when events and circumstances indicate that the assets may be impaired. If impairment is indicated, we reduce the carrying value of the asset to fair value. As of June 30, 2004, we have prepaid approximately $6.0 million to Abbott Laboratories for royalties related to the µARCS screening technology. This prepayment is carried on our balance sheet as prepaid royalty. In the first quarter of 2004 we began amortization of this asset using a five-year life as we have begun to derive value from the related technology. This technology has been evaluated by several companies including a major pharmaceutical company and based on these evaluations and potential revenues from these and other potential customers, we believe that the carrying value of the asset is not impaired. If we are not successful in generating sufficient revenues in the future from this asset, we may be required to record impairment charges up to $5.4 million.

Results of Operations For The Three Months Ended June 30, 2004 and 2003

Revenue. Total revenues increased 16%, or $1.8 million, from $11.2 million for the three months ended June 30, 2003 to $13.0 million for the three months ended June 30, 2004. The increase in revenue was primarily due to increases in chemistry services revenue, screening services revenue and instrumentation product revenue. The increase in chemistry services revenue was due to increases in deliverables under our agreement with Pfizer and the addition of a new FTE chemistry service agreement, which began in April 2004. The increase in screening services revenue was due primarily to new contracts as well as additional services provided under existing contracts in comparison to the second quarter of 2003. The increase in instrumentation product revenue was due to the launch of the Crystal Farm product in 2003, which generated significantly more sales in the second quarter of 2004 compared to the second quarter of 2003. This increase was partially offset by a decrease in revenues generated from our X-Kan contract with GlaxoSmithKline as this project was completed in April 2004.

In the second quarter of 2004 and 2003, 58% and 64%, respectively, of our revenue came from our chemistry contract with Pfizer, and we anticipate that this contract will continue to provide for a significant percentage of our revenue throughout 2004 and 2005. As of June 30, 2004, 69% of total potential revenue under our Pfizer agreement remains to be earned and recognized. Pfizer has the right to terminate the contract without cause after January 5, 2005 by giving six months’ notice.

Gross margin. Gross margin as a percentage of revenues increased from 35% for the three months ended June 30, 2003 to 40% for the three months ended June 30, 2004. The increase in gross margin for the second quarter of 2004 is primarily due to improvement in gross margins on screening, instrumentation product revenues and chemistry services. Gross margin as a percentage of screening revenue increased due to an increase in volume. Gross margin as a percentage of instrumentation product revenues increased due primarily to higher margins earned on new products compared to our historical product lines. Gross margin as a percentage of chemistry services revenue increased due to higher margins on new revenue sources under the Pfizer agreement partially offset by unabsorbed overhead resulting from lower production volumes.

Research and development expenses. Research and development expenses consist primarily of salaries and benefits, supplies and expensed development materials, facilities costs and equipment depreciation. Research and

development expenses increased 36%, or $237,000, from $663,000 for the three months ended June 30, 2003 to $900,000 for the three months ended June 30, 2004. Research and development expenses increased primarily due to the completion of customer funded research and development activities and an increase in internal programs focused on Crystal Farm product and drug discovery process development.

Selling, general and administrative expenses. Selling, general and administrative expenses consist primarily of salaries and benefits for sales and marketing and administrative personnel, advertising and promotional expenses, professional services, and facilities costs. Selling, general and administrative expenses increased 6%, or $197,000, from $3.4 million for the three months ended June 30, 2003 to $3.6 million for the three months ended June 30, 2004 due primarily to an increase in business development activities, insurance costs and professional services fees. These increases were partially offset by savings resulting from the closure of our Tucson facility in April 2003 and decreased incentive compensation costs.

Stock-based compensation. During 1999 and 2000, we granted stock options with exercise prices that were less than the estimated fair value of the underlying shares of common stock on the date of grant. Additionally, we awarded 52,500 shares of restricted stock and rights to acquire 190,000 shares of restricted stock in August 2003. As a result, we have recorded deferred stock-based compensation to be amortized on an accelerated basis over the period that these options, restricted stock grants and rights to acquire restricted stock vest. The deferred stock-based compensation expense for the three months ended June 30, 2004 was approximately $135,000, compared to approximately $75,000 for the three months ended June 30, 2003. We expect deferred compensation expense for 2004 to be approximately $900,000, inclusive of the costs related to the restricted stock grant made in July 2004.

Interest income. Interest income, net, decreased 34%, or $152,000, from $448,000 for the three months ended June 30, 2003 to $296,000 for the three months ended June 30, 2004 due primarily to realized losses incurred in the second quarter of 2004 compared to realized gains in the second quarter of 2003, as well as lower U.S. interest rates.

Results of Operations For The Six Months Ended June 30, 2004 and 2003

Revenue. Total revenues increased 4%, or $855,000, from $24.0 million for the six months ended June 30, 2003 to $24.8 million for the six months ended June 30, 2004. The increase in revenue was primarily due to increases in screening services revenue and instrumentation product revenue offset by decreases in chemistry services revenue. The decrease in chemistry services revenue was due to reductions in deliverables under two significant chemistry services agreements as well as the absence of a contract termination fee earned in the first quarter of 2003. The decreases were partially offset by an additional FTE chemistry service agreement, which began in April 2004, and new revenue sources under the Pfizer agreement. The increase in screening services revenue was due primarily to new contracts as well as additional services provided under existing contracts in comparison to the first half of 2003. The increase in instrumentation product revenue was due to the launch of the Crystal Farm product in 2003, which generated significantly more sales in the first half of 2004 compared to the first half of 2003. This increase was partially offset by a decrease in revenues generated from our X-Kan contract with GlaxoSmithKline as this project was completed in April 2004.

In the six months ended June 30, 2004 and 2003, 54% and 59%, respectively, of our revenue came from our chemistry contract with Pfizer, and we anticipate that this contract will continue to provide for a significant percentage of our revenue throughout 2004 and 2005. As of June 30, 2004, 69% of total potential revenue under our Pfizer agreement remains to be earned and recognized. Pfizer has the right to terminate the contract without cause after January 5, 2005 by giving six months’ notice.

Gross margin. Gross margin as a percentage of revenues increased from 32% for the six months ended June 30, 2003 to 42% for the six months ended June 30, 2004. The increase in gross margin for the second half of 2004 is primarily due to improvement in gross margins on chemistry services, screening and instrumentation product revenues. Gross margin as a percentage of chemistry services revenue increased primarily due to changes in our agreement with Pfizer. Under our prior agreement with Pfizer, we were compensated separately for the development and delivery of the compounds, and accordingly, our development costs were expensed as incurred. Under the amended agreement, we now bear the development risk of the compounds and are compensated upon

delivery of the compounds. A significant portion of the costs associated with the development of the compounds delivered to Pfizer in the first quarter of 2004 was expensed in prior periods in accordance with our accounting policies as applied to the prior agreement, improving our gross margin percentage in the first quarter of 2004 for these compounds. This increase in gross margin was partially offset by unabsorbed overhead costs resulting from lower production volumes in the first half of 2004. Gross margin as a percentage of screening revenue increased due to an increase in volume. Gross margin as a percentage of instrumentation product revenues increased due primarily to higher margins earned on new products compared to our historical product lines.

Research and development expenses. Research and development expenses consist primarily of salaries and benefits, supplies and expensed development materials, and facilities costs and equipment depreciation. Research and development expenses increased 31%, or $426,000, from $1.4 million for the six months ended June 30, 2003 to $1.8 million for the six months ended June 30, 2004. Research and development expenses increased primarily due to the completion of customer funded research and development activities and an increase in internal programs focused on Crystal Farm product and drug discovery process development.

Selling, general and administrative expenses. Selling, general and administrative expenses consist primarily of salaries and benefits for sales and marketing and administrative personnel, advertising and promotional expenses, professional services, and facilities costs. Selling, general and administrative expenses increased 11%, or $686,000, from $6.5 million for the six months ended June 30, 2003 to $7.2 million for the six months ended June 30, 2004 due primarily to an increase in business development activities, insurance costs and professional services fees. These increases were partially offset by savings resulting from the closure of our Tucson facility in April 2003 and decreased incentive compensation costs.

Stock-based compensation. During 1999 and 2000, we granted stock options with exercise prices that were less than the estimated fair value of the underlying shares of common stock on the date of grant. Additionally, we awarded 52,500 shares of restricted stock and rights to acquire 190,000 shares of restricted stock in August 2003. As a result, we have recorded deferred stock-based compensation to be amortized on an accelerated basis over the period that these options, restricted stock grants and rights to acquire restricted stock vest. The deferred stock-based compensation expense for the six months ended June 30, 2004 was approximately $304,000, compared to approximately $160,000 for the six months ended June 30, 2003. We expect deferred compensation expense for 2004 to be approximately $900,000, inclusive of the costs related to the restricted stock grant made in July 2004.

Interest income. Interest income, net, decreased 36%, or $360,000, from $993,000 for the six months ended June 30, 2003 to $633,000 for the six months ended June 30, 2004 due primarily to realized losses incurred in the first half of 2004 compared to realized gains in the first half of 2003, as well as lower U.S. interest rates.

Liquidity and Capital Resources

Since inception of the Company, we have funded our operations principally with $39.0 million of private equity financings and $94.7 million of net proceeds from our initial public offering in July 2000. In May 2004, we raised approximately $5.1 million in net proceeds from the sale of 1,083,300 shares of common stock in a public offering.

At June 30, 2004, cash and cash equivalents and short-term investments totaled approximately $77.9 million, compared to $72.6 million at December 31, 2003.

Operating Activities. We rely on cash flows from operations to provide working capital for current and future operations. We believe we have sufficient cash resources to fund existing operations through 2005. Cash flows from operating activities totaled $1.5 million and $4.8 million for the six months ended June 30, 2004 and 2003, respectively. The decrease in operating cash flows in 2004 compared to 2003 was primarily due to a significant increase in annual incentives paid to key employees in the first quarter of 2004 compared to 2003, a decrease in prepayments received from our customers, an increase in inventory and an increase in accounts receivable offset partially by improved operating results. We expect continued decreases in prepayments and, to the extent we are able

to achieve our revenue goals for the remainder of 2004, increases in accounts receivable and inventory in 2004, which could negatively impact our cash flows from operations in the future.

Investing Activities. Cash used in investing activities totaled $8.0 million and $7.4 million for the six months ended June 30, 2004 and 2003, respectively. The increase in cash used in investing activities is due primarily to our investing the net proceeds from the sale of approximately 1.1 million shares of our common stock which occurred during the second quarter of 2004 offset by a $2.0 million royalty prepayment made in the first quarter of 2003 as required under our exclusive µARCS license agreement with Abbott Laboratories, which we carry on the balance sheet as prepaid royalty. No additional prepayments are required under this agreement.

We currently anticipate investing between approximately $1.5 million to $2.0 million during the remainder of 2004 for leasehold improvements and capital equipment necessary to support future revenue growth. Our actual future capital requirements will depend on a number of factors, including our success in increasing sales of both existing and new products and services, expenses associated with unforeseen litigation, regulatory changes, competition and technological developments, and potential future merger and acquisition activity as well as research and development spending.

Financing Activities. Cash provided by financing activities totaled $5.4 million for the six months ended June 30, 2004 compared to cash used in financing activities for the six months ended June 30, 2003 of $510,000. This change is primarily due to sale of approximately 1.1 million shares of our common stock generating $5.1 million in net proceeds during the second quarter of 2004. Historically, we had debt obligations under lease and line of credit agreements. Net payments made under these agreements totaled $448,000 in the first half of 2003. As of June 30, 2004, we have no debt obligations. Absent any significant merger and acquisition activity, we do not expect to incur debt in 2004.

On October 4, 2001, our board of directors authorized a Stock Repurchase Plan, authorizing us to repurchase up to 2,000,000 shares of common stock at no more than $3.50 per share. In the six months ended June 30, 2003, we purchased 115,000 shares under this Plan for $289,000. No shares were repurchased in the six months ended June 30, 2004. We have the authority to purchase additional shares in the future.

RISKS AND UNCERTAINTIES

In addition to the other information contained herein, you should carefully consider the following risk factors in evaluating our company.

We derive a significant percentage of our revenues from a single customer. If this customer relationship terminated, we could have difficulty finding customers that would purchase our products and services in sufficient amounts to replace the capacity and lost revenues resulting from this significant customer.

We anticipate that a significant portion of our revenues for 2004 and 2005 will be derived from the chemistry collaboration we entered into with Pfizer originally in December 2001. In February 2004, the agreement with Pfizer was amended. Under this agreement, Pfizer has a contractual right to terminate the contract, with or without cause, upon six months notice after January 5, 2005. Either party may also terminate the agreement upon the material, uncured breach of the other party, and Pfizer may terminate the agreement if we are acquired by a third party or in the event of a change in control of our company. During the first half of 2004, revenue from Pfizer represented 54% of our total revenue. As of June 30, 2004, 69% of total potential revenue under the new Pfizer agreement remains to be earned and recognized. If our relationship with Pfizer or our contracts with other customers to whom we provide significant products or services are terminated, we will have substantial capacity available until we are able to find new customers for our products and services to utilize that capacity. We may be delayed in entering or not able to enter into contracts with new customers to utilize any available capacity. We will continue to bear the costs of that capacity until we are able to enter into contracts with customers for those products or services. Revenues with respect to those products and services may be delayed or we may not recognize revenues at all to the extent we are delayed in entering or not able to enter into contracts with new customers to utilize available capacity.

The drug discovery industry is highly competitive and subject to technological change, and we may not have the resources necessary to compete successfully.

We compete with companies in the United States and abroad that engage in the development and production of drug discovery products and services. These competitors include companies engaged in the following areas of drug discovery:

• Assay development and screening;

• Combinatorial chemistry instruments;

• Crystallography incubation and imaging systems;

• Compound libraries and lead optimization;

• Informatics; and

• Gene profiling.

Academic institutions, governmental agencies and other research organizations also conduct research in areas in which we provide services, either on their own or through collaborative efforts. Also, substantially all of our pharmaceutical and biopharmaceutical company customers have internal departments that provide some or all of the products and services we sell, so these customers may have limited needs for our products and services. Many of our competitors have more experience and have access to greater financial, technical, research, marketing, sales, distribution, service and other resources than we do. We may not yet be large enough to achieve satisfactory market recognition or operating efficiencies, particularly in comparison to some competitors.

Moreover, the pharmaceutical and biopharmaceutical industries are characterized by continuous technological innovation. We anticipate that we will face increased competition in the future as new companies enter the market and our competitors make advanced technologies available. Technological advances or entirely different approaches that we or one or more of our competitors develop may render our products, services and expertise obsolete or uneconomical. For example, advances in informatics and virtual screening may render some of our technologies, such as our large compound libraries, obsolete. Additionally, the existing approaches of our competitors or new approaches or technologies that our competitors develop may be more effective than those we develop. We may not be able to compete successfully with existing or future competitors.

In addition, due to improvements in global communications, combined with the supply of lower cost PhD level scientific talent, we face the growing threat of competition for our chemistry and computational chemistry services from low-cost offshore locations such as China, India and Eastern Europe.

If we do not generate adequate revenues from our µARCS investment in the near future, we may have to record significant impairment charges.

We have prepaid approximately $6.0 million to Abbott Laboratories for royalties related to the µARCS screening technology. This prepayment is carried on our balance sheet as prepaid royalty net of $0.6 million of accumulated amortization. If we are not successful in generating revenues in the future from this asset, we may be required to record impairment charges up to $5.4 million, which would materially impact our profitability.

Our financial performance will depend on the prospects of the pharmaceutical and biopharmaceutical industries and the extent to which these industries engage outside parties to perform one or more aspects of their drug discovery process.

Our revenues depend to a large extent on research and development expenditures by the pharmaceutical and biopharmaceutical industries and companies in these industries outsourcing research and development projects. These expenditures are based on a wide variety of factors, including the resources available for purchasing research equipment, the spending priorities among various types of research and policies regarding expenditures during recessionary periods. In recent years, pharmaceutical companies have been attempting to contain spending on drug discovery and many biotechnology companies have found it difficult to raise capital to fund drug discovery activities. Geopolitical uncertainty or general economic downturns in our customers’ industries or any decrease in research and development expenditures could harm our operations, as could increased acceptance of management theories that counsel against outsourcing of critical business functions. Any decrease in drug discovery spending by pharmaceutical and biopharmaceutical companies could cause our revenues to decline and hurt our profitability.

The concentration of the pharmaceutical industry and the current trend toward increasing consolidation could hurt our business prospects.

The pharmaceutical customer segment of the market for our products and services is highly concentrated, with approximately 50 large pharmaceutical companies conducting drug discovery research. We have lost customers due to consolidation of pharmaceutical companies and the continuation of this trend may reduce the number of our current and potential customers even further. As a result, a small number of customers could account for a substantial portion of our revenues. In addition, because of the heavy concentration of the pharmaceutical industry and the relatively high cost of our systems, such as NanoKan, µARCS and Crystal Farm, we expect there will be only a limited number of potential buyers for these systems.

Additional risks associated with a concentrated customer base include:

• larger companies may develop and utilize in-house technology and expertise rather than using our products and services; and

• larger customers may negotiate price discounts or other terms for our products and services that are unfavorable to us.

We may not achieve or maintain profitability in the future.

We have incurred significant operating and net losses since our inception. As of June 30, 2004, we had an accumulated deficit of $101.8 million. Although we generated net income for the three and six months ended June 30, 2004 of approximately $740,000 and $1.8 million, respectively and for the year ended December 31, 2003 of $1.1 million, we had net losses of $62.1 million and $11.1 million for the years ended December 31, 2002 and 2001, respectively. We may also in the future incur operating and net losses and negative cash flow from operations. We did not achieve operating profitability until the third quarter of 2003 and we may not be able to achieve or maintain profitability in any quarter in the future. Moreover, if we do achieve profitability, the level of any profitability cannot be predicted and may vary significantly from quarter to quarter.

Our discontinuation of the development of chemical compounds to be sold out of inventory places more emphasis on integrated drug discovery collaborations, an area of higher risk and complexity.

As a result of our decision to limit access to our proprietary chemistry compounds and capabilities solely to companies that enter into integrated drug discovery, chemistry or screening and optimization collaborations with us, we now rely on this relatively complex form of customer engagement to generate revenue. As a result of the inherent complexity of such collaborations, we have an increased risk of being unable to reach agreement with the prospective

customer for such collaborations or of structuring sub-optimal arrangements that fail to adequately compensate us for the risks inherent in such collaborations.

We may fail to expand customer relationships through the integration of products and services.

We may not be able to use existing relationships with customers in individual areas of our business to sell products and services in multiple areas of drug discovery. We may not be successful in selling our offerings in combination across the range of drug discovery disciplines we serve because integrated combinations of our products and services may not achieve time and cost efficiencies for our customers, especially our large pharmaceutical company customers. Biotechnology companies may desire our integrated offerings but are often not sufficiently capitalized to pay for these services. In addition, we may not succeed in further integrating our offerings. If we do not achieve integration of our products and services, we may not be able to take advantage of potential revenue opportunities and differentiate ourselves from competitors.

Our products, services and technologies may never help discover drugs that receive Food and Drug Administration approval, which may make it difficult for us to gain new business.

To date, we are not aware of any of our customers having used any of our drug discovery products, services or technologies to develop a drug that ultimately has been approved by the Food and Drug Administration, and our customers may never do so. Whether our customers use our drug discovery products, services and technologies to develop any drugs that ultimately receive Food and Drug Administration approval will depend heavily on our scientific success and our customers’ scientific success, as well as on our customers’ ability to meet applicable Food and Drug Administration regulatory requirements. Our products, services and technologies may fail to assist our customers in achieving their drug discovery objectives, either on a timely basis or at all. For example, when our customers deliver proteins to us for assay development or chemistry library design ideas for chemical compound development and production, we may design assays or develop chemical compound libraries that fail to fully characterize the applicable protein’s or compound’s therapeutic potential, which could cause its further development to be delayed or abandoned. Additionally, our customers may not deliver to us proteins for assay development or chemistry library design ideas for chemical compound development and production that yield promising lead compounds for further development. Our customers may also lack the resources or experience or be otherwise unable to comply with the Food and Drug Administration’s clinical trial requirements. Certain of our competitors are able to claim that their drug discovery products or services have been used in developing drugs that received Food and Drug Administration approval. To the extent that potential customers consider demonstrated therapeutic success an important factor in selecting between us and our competitors, we may be competitively disadvantaged, which would negatively impact our ability to generate new business.

Our financial performance will depend on improved market conditions in the segments of the drug discovery and development process in which we participate.

The drug discovery and development process can be broadly separated into the following stages: Target identification; target validation; lead discovery; lead optimization; pre-clinical development; IND filing; clinical trials, phases I-III; new drug application, or NDA; and post market surveillance. We currently participate in the areas of lead discovery and lead optimization. Based on current industry averages, the cost of acquiring a validated target plus the costs of lead discovery and lead optimization are greater than the expected proceeds of out-licensing a potential drug candidate during the pre-clinical phase of drug development. This is primarily due to the negative imbalance between the relatively high cost of obtaining pre-clinical drug candidates, the high failure rate of such pre-clinical candidates, and the relatively low demand for such pre-clinical candidates that exists at present. It is estimated that a positive expected return on investment is not obtained until a drug candidate has passed through phase II clinical trials, which requires a significant commitment of resources to attain. Therefore, many drug companies may be deterred from engaging in drug discovery unless they have the substantial financial resources necessary to fund the drug discovery process all the way through phase II clinical trials. Unless advances are made to either reduce the cost or improve the success rate of pre-clinical drug candidates, or unless the market demand for such pre-clinical drug candidates

improves, we might continue to face difficult market conditions for our products and services which might inhibit our growth.

We may not be able to achieve and maintain success in our offshore operations.

We entered into a research and development collaboration agreement under which we utilize scientists and equipment at a subcontractor’s facility located in India to take advantage of a lower cost structure. However, we may not be able to achieve or maintain a successful relationship in this offshore location or realize lower costs. Additionally, such offshore business could suffer due to the geographical, time and distance challenges as well as cultural difficulties of managing such an operation, which could cause delays, customer dissatisfaction or other issues.

Many of our products and services have lengthy sales cycles, which could cause our operating results to fluctuate significantly from quarter to quarter.

Sales of many of our products and services typically involve significant technical evaluation and commitment of expense or capital by our customers. Accordingly, the sales cycles, or the time from finding a prospective customer through closing the sale, associated with these products or collaborations, typically range from six to eighteen months. Sales of these products and the formation of these collaborations are subject to a number of significant risks, including customers’ budgetary constraints and internal acceptance reviews that are beyond our control. Due to these lengthy and unpredictable sales cycles, our operating results could fluctuate significantly from quarter to quarter. We expect to continue to experience significant fluctuations in quarterly operating results due to a variety of factors, such as general and industry specific economic conditions, that may affect the research and development expenditures of pharmaceutical and biopharmaceutical companies.

Our products and services involve significant scientific risk of fulfillment.

A large portion of our revenues relies upon our and our customers’ scientific success. Our products, services and technologies may fail to assist our customers in achieving their drug discovery objectives, on a timely basis or at all. For example, when our customers deliver proteins to us for assay development or chemistry library design ideas for chemical compound development and production, we rely on our customers for timely delivery of those deliverables, and our customers rely on us for timely and effective assay design or compound library development and production that fulfills our scientific obligations to them. To the extent that either we experience delays or failures in receiving specific deliverables required for us to complete our objectives or we encounter delays in our ability to meet, or are unable to meet, our scientific obligations, we may be unable to receive and recognize revenues in accordance with our expectations.

If our revenues decline or do not grow as anticipated, we might not be able to correspondingly reduce our operating expenses.

A large portion of our expenses, including expenses for facilities, equipment and personnel, is relatively fixed. Accordingly, if revenues decline or do not grow as anticipated, we might not be able to correspondingly reduce our operating expenses. Failure to achieve anticipated levels of revenues could therefore significantly harm our operating results for a particular fiscal period.

Due to the possibility of fluctuations in our revenues (on an absolute basis and relative to our expenses), we believe that quarter-to-quarter comparisons of our operating results are not a reliable indication of our future performance.

If our products and services do not become widely used in the pharmaceutical and biopharmaceutical industries, it is unlikely that we will be profitable.

We have a limited history of offering our products and services, including informatics tools, biology services, µARCS, toxicology services, Crystal Farm and combinatorial chemistry instrumentation systems. It is uncertain

whether our current customers will continue to use these products and services or whether new customers will use these products and services. In order to be successful, our products and services must meet the requirements of the pharmaceutical and biopharmaceutical industries, and we must convince potential customers to use our products and services instead of competing technologies and offerings. Moreover, we cannot thrive unless we can achieve economies of scale on our various offerings. Market acceptance will depend on many factors, including our ability to:

• convince potential customers that our technologies are attractive alternatives to other technologies for drug discovery;

• manufacture products and conduct services in sufficient quantities with acceptable quality and at an acceptable cost;

• convince potential customers to purchase drug discovery products and services from us rather than developing them internally; and

• place and service sufficient quantities of our products.

Because of these and other factors, some of which are beyond our control, our products and services may not gain sufficient market acceptance.

The intellectual property rights on which we rely to protect the technology underlying our products and techniques may not be adequate, which could enable third parties to use our technology or very similar technology and could reduce our ability to compete in the market.

Our success will depend, in part, on our ability to obtain, protect and enforce patents on our technology and to protect our trade secrets. We also depend, in part, on patent rights that third parties license to us. Any patents we own or license may not afford meaningful protection for our technology and products. Others may challenge our patents or the patents of our licensors and, as a result, these patents could be narrowed, invalidated or rendered unenforceable. In addition, current and future patent applications on which we depend may not result in the issuance of patents in the United States or foreign countries. Competitors may develop products similar to ours that are not covered by our patents. Further, since there is a substantial backlog of patent applications at the U.S. Patent and Trademark Office, the approval or rejection of our or our competitors’ patent applications may take several years.

Our European eukaryotic gene profiling patent was opposed by various companies. Oral proceedings were held before the Opposition Division of the European Patent Office in January 2003. At the conclusion of the hearing, the Opposition Division maintained our patent in amended form. The period during which an appeal of the Opposition Division decision could be made has expired. As amended, the patent claims kits and methods for identifying and characterizing the potential toxicity of a compound using expression profiles of four categories of stress.

In addition to patent protection, we also rely on copyright protection, trade secrets, know-how, continuing technological innovation and licensing opportunities. In an effort to maintain the confidentiality and ownership of our trade secrets and proprietary information, we require our employees, consultants and advisors to execute confidentiality and proprietary information agreements. However, these agreements may not provide us with adequate protection against improper use or disclosure of confidential information, and there may not be adequate remedies in the event of unauthorized use or disclosure. Furthermore, like many technology companies, we may from time to time hire scientific personnel formerly employed by other companies involved in one or more areas similar to the activities conducted by us. In some situations, our confidentiality and proprietary information agreements may conflict with, or be subject to, the rights of third parties with whom our employees, consultants or advisors have prior employment or consulting relationships.

We acquired an exclusive license to the µARCS technology from Abbott Laboratories. The µARCS technology provides high throughput screening of compounds against a very broad range of drug discovery targets. Under the license agreement, Abbott is required to seek patent coverage for the licensed technology. If any license

disputes arise between us and Abbott relating to the µARCS technology and we are not able to resolve those disputes, or if Abbott is unsuccessful in obtaining adequate patent coverage for the µARCS technology, our ability to screen compounds may be compromised and we may not be able to prevent competitors, including Abbott, from using the µARCS technology, which could have a material adverse effect on our financial condition and results of operations.

Although we require our employees and consultants to maintain the confidentiality of all confidential information of previous employers, their prior affiliations may subject us or these individuals to allegations of trade secret misappropriation or other similar claims. Finally, others may independently develop substantially equivalent proprietary information and techniques, or otherwise gain access to our trade secrets. Our failure to protect our proprietary information and techniques may inhibit or limit our ability to exclude certain competitors from the market.

The drug discovery industry has a history of intellectual property litigation and we may be involved in intellectual property lawsuits, which may be lengthy and expensive.

In order to protect or enforce our patent rights, we may have to initiate legal or administrative proceedings against third parties. In addition, others may sue us or initiate interference proceedings against us for infringing their intellectual property rights, or we may find it necessary to initiate a lawsuit seeking a declaration from a court that we are not infringing the proprietary rights of others. The patent positions of pharmaceutical, biopharmaceutical and drug discovery companies are generally uncertain. A number of pharmaceutical companies, biopharmaceutical companies, independent researchers, universities and research institutions may have filed patent applications or may have been granted patents that cover technologies similar to the technologies owned by, or licensed to, us or our collaborators. A number of patents may have been issued or may be issued in the future that could cover certain aspects of our technology and that could prevent us from using technology that we use or expect to use. In addition, we are unable to determine all of the patents or patent applications that may materially affect our ability to make, use or sell any potential products. Legal or administrative proceedings relating to intellectual property would be expensive, take significant time and divert management’s attention from other business concerns, no matter whether we win or lose. The cost of such litigation, interference or administrative proceedings could hurt our profitability.

Further, an unfavorable judgment in an administrative proceeding, interference or infringement lawsuit brought against us, in addition to any damages we might have to pay, could prevent us from obtaining intellectual property protection for our technology, require us to stop the infringing activity or obtain a license. Any required license may not be available to us on acceptable terms, or at all. In addition, some licenses may be nonexclusive, and therefore, our competitors may have access to the same technology that is licensed to us. If we fail to obtain a required license or are unable to design around a patent, we may be unable to sell some of our products or services.

Our stock price will likely be volatile.

The trading price of our common stock has been and will likely continue to be volatile and could be subject to fluctuations in price in response to various factors, many of which are beyond our control, including:

• actual or anticipated variations in quarterly operating results;

• announcements of technological innovations by us or our competitors;

• new products or services introduced or announced by us or our competitors;

• changes in financial estimates by (or the beginning or cessation of research coverage by) securities analysts;

• the announcements by us or our competitors of financial results that do not meet or exceed the results anticipated by the public markets;

• conditions or trends in the pharmaceutical and biopharmaceutical industries or in the drug discovery services industry;

• announcements by us or our competitors of significant acquisitions, collaborations, joint ventures or capital commitments, or terminations of collaborations or joint ventures;

• the implementation or wind-down of stock buyback programs;

• additions or departures of key personnel;

• economic and political factors; and

• sales of our common stock, including sales by any of our stockholders who beneficially own more than 5% of our common stock and who could potentially sell large amounts of our common stock at any one time.

In addition, price and volume fluctuations in the stock market in general, and the Nasdaq National Market and the market for technology companies in particular, have often been unrelated or disproportionate to the operating performance of those companies. Further, the market prices of securities of life sciences companies have been particularly volatile. Conditions or trends in the pharmaceutical and biopharmaceutical industries generally may cause further volatility in the trading price of our common stock, because the market may incorrectly perceive us as a pharmaceutical or biopharmaceutical company and our customers are pharmaceutical and biopharmaceutical companies. These broad market and industry factors may harm the market price of our common stock, regardless of our operating performance. In the past, plaintiffs have often instituted securities class action litigation following instances of volatility in the market price of a company’s securities. A securities class action suit against us could result in potential liabilities, substantial costs and the diversion of management’s attention and resources, regardless of whether we win or lose.

Our customers may restrict our use of scientific information, which could prevent us from using this information for additional revenue.

We plan to generate and use information that is not proprietary to our customers and which we derive from performing drug discovery services for our customers. However, our customers may not allow us to use information such as the general interaction between types of chemistries and types of drug targets that we generate when performing drug discovery services for them. Our current contracts typically restrict our use of certain scientific information we generate for our customers, such as the biological activity of chemical compounds with respect to drug targets, and future contracts also may restrict our use of additional scientific information. To the extent that our use of information is restricted, we may not be able to collect and aggregate scientific data and take advantage of potential revenue opportunities.

Our ability to grow will depend on our attracting and retaining key executives, experienced scientists and sales personnel.

Our future success will depend to a significant extent on our ability to attract, retain and motivate highly skilled scientists and sales personnel. In addition, our business would be significantly harmed if we lost the services of Riccardo Pigliucci, our chief executive officer. We do not maintain life insurance on any of our officers. Our ability to maintain, expand or renew existing collaborations with our customers, enter into new collaborations and provide additional services to our existing customers depends, in large part, on our ability to hire and retain scientists with the skills necessary to keep pace with continuing changes in drug discovery technologies and sales personnel who are highly motivated. Additionally, it is difficult for us to find qualified sales personnel in light of the fact that our sales personnel generally hold PhD’s in scientific fields. Our U.S. employees are “at will,” which means that they may resign at any time, and we may dismiss them at any time (subject, in some cases, to severance payment obligations). We believe that there is a shortage of, and significant competition for, scientists with the skills and experience in the

sciences necessary to perform the services we offer. We compete with pharmaceutical companies, biopharmaceutical companies, combinatorial chemistry companies, contract research companies and academic institutions for new personnel. If we do not attract new scientists or sales personnel or retain or motivate our existing personnel, we will not be able to grow.

We have acquired several businesses and face risks associated with integrating these businesses and potential future acquisitions.

We have acquired several businesses and plan to continue to review potential acquisition candidates in the ordinary course of our business, and our strategy includes building our business through acquisitions. Acquisitions involve numerous risks, including, among others, difficulties and expenses incurred in the consummation of acquisitions and assimilation of the operations, personnel and services or products of the acquired companies, difficulties of operating new businesses, the diversion of management’s attention from other business concerns and the potential loss of key employees of the acquired company. In addition, acquired businesses may have management structures incompatible with our own and may experience difficulties in maintaining their existing levels of business after joining us. If we do not successfully integrate and grow the businesses we have acquired or any businesses we may acquire in the future, our business will suffer. Additionally, acquisition candidates may not be available in the future or may not be available on terms and conditions acceptable to us. Acquisitions of foreign companies also may involve additional risks of assimilating different business practices, overcoming language and cultural barriers and foreign currency translation. We currently have no agreements or commitments with respect to any acquisition, and we may never successfully complete any additional acquisitions.

We may incur write-downs or write-offs in connection with potential future acquisitions, and exit costs, losses and liabilities in connection with potential future business divestitures or shut-downs.

We incurred a $50.9 million goodwill impairment charge during the fourth quarter of 2002, which represented the write-off of goodwill that we had accumulated in connection with several acquisitions. In the event that we make future acquisitions, we may take additional write-downs or write-offs associated with acquired assets, which could have a material adverse effect on our results of operations and financial condition. Any future acquisitions we make may also not improve our business as much as we expect, or be accretive to our earnings, which could cause the trading price of our common stock to decline. In addition, if any future acquisitions we make do not improve our business as much as we expect, we may choose to discontinue the businesses associated with those acquisitions by divestiture or by shutting those businesses down. We may also choose to divest or shut down existing businesses or product or service lines for strategic reasons. We may incur substantial exit costs, losses and liabilities in connection with any such divestiture or shut-down.

Our success will depend on our ability to manage growth and expansion.

Growth in our operations has placed and, if we grow in the future, will continue to place a significant strain on our operational, human and financial resources. We intend to continue to grow our business internally and by acquisition. As and if we expand our operations we will not necessarily have in place infrastructure and personnel sufficient to accommodate the increased size of our business. Our ability to effectively manage any growth through acquisitions or any internal growth will depend, in large part, on our ability to hire, train and assimilate additional management, professional, scientific and technical personnel and our ability to expand, improve and effectively use our operating, management, marketing and financial systems to accommodate our expanded operations. These tasks are made more difficult as we acquire businesses in geographically disparate locations.

Our operations could be interrupted by damage to our facilities.

Our results of operations are dependent upon the continued use of our highly specialized laboratories and equipment. Our operations are primarily concentrated in facilities in San Diego, California, South San Francisco, California and Allschwil, Switzerland. Natural disasters, such as earthquakes or fires, or terrorist acts could damage our laboratories or equipment and these events may materially interrupt our business. We maintain business interruption

insurance to cover lost revenues caused by such occurrences. However, this insurance would not compensate us for the loss of opportunity and potential adverse impact on relations with existing customers created by an inability to meet our customers’ needs in a timely manner, and may not compensate us for the physical damage to our facilities.

We have accrued significant net operating loss carryforwards that we believe we will not be able to fully use.

At December 31, 2003, we had federal and California income tax net operating loss carryforwards of approximately $21.8 million and $14.5 million, respectively. The federal and California tax loss carryforwards will begin to expire in 2010 and 2005, respectively, unless previously utilized. We believe that our ability to utilize our net operating loss carryforwards may be substantially restricted by the limitations of Section 382 of the Internal Revenue Code which apply when there are certain changes in ownership of a corporation. To the extent we begin to realize significant taxable income, these limitations may result in our incurring federal income tax liability notwithstanding the existence of otherwise available carryforwards. To date we have not quantified the potential impact of these limitations.

We are subject to foreign currency risk related to conducting business in multiple currencies.

Currency fluctuations between the U.S. dollar and the currencies in which we do business, including the British pound, the Japanese yen, the Swiss franc, the Euro and the Indian rupee, will cause foreign currency translation gains and losses. We cannot predict the effects of exchange rate fluctuations on our future operating results because of the number of currencies involved, changes in the percentage of our revenue that will be invoiced in foreign currencies, the variability of currency exposure and the potential volatility of currency exchange rates. Because we conduct business in multiple currencies we are subjected to economic and earnings risk. We do not currently engage in foreign exchange hedging transactions to manage our foreign currency exposure; however, we may begin to hedge certain transactions between the Swiss franc and other currencies that are invoiced from our Swiss affiliate in order to minimize foreign exchange transaction gains and losses.

We may be subject to liability regarding hazardous materials.

Our products and services as well as our research and development processes involve the controlled use of hazardous materials. For example, we often use dangerous acids, bases, oxidants, radio isotopic and flammable materials. We are subject to federal, state and local laws and regulations governing the use, manufacture, storage, handling and disposal of such materials and certain waste products. We cannot completely eliminate the risk of accidental contamination or injury from these materials. In the event of such an accident, we could be held liable for any damages that result, and any such liability could exceed our resources and disrupt our business. In addition, we may have to incur significant costs to comply with environmental laws and regulations related to the handling or disposal of such materials or waste products in the future, which would require us to spend substantial amounts of money.

Because it is unlikely that we will pay dividends, our stockholders will only be able to benefit from holding our stock if the stock price appreciates.

We have never paid cash dividends on our capital stock and do not anticipate paying any cash dividends in the foreseeable future.

Anti-takeover provisions in our stockholder rights plan and in our charter and bylaws could make a third-party acquisition of us difficult.

In 2003 we adopted a stockholder rights plan (a so-called “poison pill”). Also, our certificate of incorporation and bylaws contain provisions that could make it more difficult for a third party to acquire us, even if doing so would be beneficial to our stockholders. These provisions could limit the price that investors might be willing to pay in the future for shares of our common stock.

Item 3. Quantitative and Qualitative Disclosures About Market Risk

Short-term investments. Our interest income is sensitive to changes in the general level of U.S. interest rates, particularly since a significant portion of our investments are and will be in short-term marketable securities, U.S. government securities and corporate bonds. Due to the nature and maturity of our short-term investments, we have concluded that there is no material market risk exposure to our principal. The average maturity of our investment portfolio is six months. A 1% change in interest rates would have an effect of approximately $395,000 on the value of our portfolio.

Foreign currency rate fluctuations. The functional currency for our Discovery Partners International AG (DPI AG) group is the Swiss franc. DPI AG accounts are translated from their local currency to the U.S. dollar using the current exchange rate in effect at the balance sheet date for the balance sheet accounts, and using the average exchange rate during the period for revenues and expense accounts. The effects of translation for our DPI AG group are recorded as a separate component of stockholders’ equity (accumulated other comprehensive income (loss)). DPI AG conducts its business with customers in local currencies. Exchange gains and losses arising from these transactions are recorded using the actual exchange differences on the date the transaction is settled.

The functional currency for our Discovery Partners International LLC (DPI LLC) group is the Japanese yen. DPI LLC accounts are translated from their local currency to the U.S. dollar using the current exchange rate in effect at the balance sheet date for the balance sheet accounts, and using the average exchange rate during the period for revenues and expense accounts. The effects of translation for our DPI LLC group are recorded as a separate component of stockholders’ equity (accumulated other comprehensive income (loss)). DPI LLC conducts its business in local currencies. Exchange gains and losses arising from these transactions are recorded using the actual exchange differences on the date the transaction is settled.

We have not in the past taken any action to reduce our exposure to changes in foreign currency exchange rates, such as options or futures contracts, with respect to transactions with DPI AG, DPI LLC or transactions with our worldwide customers, but anticipate that we could begin to hedge against foreign exchange transaction gains and losses resulting from non-Swiss franc invoices issued to customers by DPI AG in the future. A 10% change in the value of the Swiss franc and Japanese Yen, collectively, relative to the U.S. dollar throughout 2004 would have resulted in a 2% change in revenue for the six months ended June 30, 2004.

Inflation. We do not believe that inflation has had a material impact on our business or operating results during the periods presented.

Item 4. Controls and Procedures

(a) Controls and Procedures

In order to ensure that the information we must disclose in our filings with the Securities and Exchange Commission is recorded, processed, summarized, and reported on a timely basis, we have formalized our disclosure controls and procedures. Our principal executive officer and principal financial officer have reviewed and evaluated the effectiveness of our disclosure controls and procedures, as defined in Exchange Act Rules 13a-15(e) and 15d-15(e), as of June 30, 2004. Based on such evaluation, such officers have concluded that, as of June 30, 2004, our disclosure controls and procedures were effective in timely alerting them to material information relating to us (and our consolidated subsidiaries) required to be included in our periodic SEC filings. There has been no change in our internal control over financial reporting during the quarter ended June 30, 2004 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

PART II

OTHER INFORMATION

Item 1. Legal Proceedings

None.

Item 2. Changes in Securities, Use of Proceeds and Issuer Purchases of Equity Securities

The registration statement (File No. 333-36638) for our initial public offering was declared effective by the SEC on July 27, 2000. We received net proceeds from the offering of approximately $94.7 million. Through June 30, 2004, we had used approximately $17.0 million of the net proceeds for acquisitions of companies, $6.0 million for prepaid µARCS royalties, $11.3 million for capital expenditures and $1.1 million for costs associated with restructuring.

Item 3. Defaults Upon Senior Securities

None.

Item 4. Submission of Matters to a Vote of Security Holders

We held our annual meeting of stockholders on May 13, 2004. As of March 19, 2004, the record date of our meeting, 24,638,177 shares of our common stock were outstanding and entitled to vote.

The following matters were voted upon at the meeting:

1. The stockholders elected two Directors to hold office for a term expiring upon the 2007 Annual Meeting of Stockholders:

Name of Director Elected	Shares Voting in Favor	Shares Withheld
Herm Rosenman	21,810,495	386,389
Sir Colin T. Dollery.	21,810,495	386,389

The following individuals are continuing directors with terms expiring upon the 2005 Annual Meeting of Stockholders: John P. Walker and Alan J. Lewis. The following individuals are continuing directors with terms expiring upon the 2006 Annual Meeting of Stockholders: Riccardo Pigliucci, Harry F. Hixson and Michael C. Venuti.

2. The stockholders ratified the appointment of Ernst & Young LLP as our independent auditors for the fiscal year ending December 31, 2004:

		Votes
For		21,958,491
Against		193,941
Abstaining		44,452

Item 5. Other Information

None.

Item 6. Exhibits and Reports on Form 8-K

(a) Exhibits:

Exhibit Number		Exhibit Description
3.1		Certificate of Incorporation of the Company (1)
3.2		Bylaws of the Company (1)
4.1		Specimen common stock certificate (2)
4.2		Rights Agreement, dated as of February 13, 2003, including the form of Certificate of Designation, the form of Rights Certificate and the Summary of Rights (3)
10.78†		Amendment to Worldwide Distribution and Strategic Alliance Agreement between the Company and Bruker AXS Inc., dated May 11, 2004
31.1		Certification of the Chief Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2		Certification of the Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1		Certification of the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2		Certification of the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

(1) Incorporated by Reference to the Company’s Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on June 23, 2000

(2) Incorporated by Reference to the Company’s Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on July 26, 2000

(3) Incorporated by Reference to the Company’s Report on Form 8-K filed with the Securities and Exchange Commission on February 24, 2003

† Certain confidential portions of this Exhibit were omitted by means of redacting a portion of the text (the “Mark”). This Exhibit has been filed separately with the Secretary of the Commission without the Mark pursuant to the Company’s Application Requesting Confidential Treatment under Rule 24b-2 under the Securities Exchange Act of 1934.

(b) Reports on Form 8-K:

We filed a Current Report on Form 8-K on April 20, 2004 to furnish our financial results for the first quarter, as reported in a press release dated April 20, 2004 and the script of the Chief Executive and Financial Officers’ comments from our first quarter earnings conference call.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

	DISCOVERY PARTNERS INTERNATIONAL, INC.

Date: August 6, 2004	By:	/s/	Riccardo Pigliucci
		Riccardo Pigliucci
		Chief Executive Officer
		(Duly Authorized Officer)

Date: August 6, 2004	By:	/s/	Craig Kussman
		Craig Kussman
		Chief Financial Officer,
		Senior Vice President Finance
		and Administration and Secretary
		(Principal Financial and Accounting Officer)

EXHIBIT INDEX

Exhibit Number		Exhibit Description
3.1		Certificate of Incorporation of the Company (1)
3.2		Bylaws of the Company (1)
4.1		Specimen common stock certificate (2)
4.2		Rights Agreement, dated as of February 13, 2003, including the form of Certificate of Designation, the form of Rights Certificate and the Summary of Rights (3)
10.78†		Amendment to Worldwide Distribution and Strategic Alliance Agreement between the Company and Bruker AXS Inc., dated May 11, 2004
31.1		Certification of the Chief Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2		Certification of the Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1		Certification of the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2		Certification of the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

(1) Incorporated by Reference to the Company’s Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on June 23, 2000

(2) Incorporated by Reference to the Company’s Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on July 26, 2000

(3) Incorporated by Reference to the Company’s Report on Form 8-K filed with the Securities and Exchange Commission on February 24, 2003