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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

Commission File Number: 0-19797

WHOLE FOODS MARKET, INC.

(Exact name of registrant as specified in its charter)

601 North Lamar Blvd., Suite 300

Austin, Texas 78703

(Address of principal executive offices)

Registrant’s telephone number, including area code:

512-477-4455

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 x                         No ¨

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

Yes x                         No ¨

The number of shares of the registrant’s common stock, no par value, outstanding as of May 9, 2004 was 61,822,332 shares.

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Whole Foods Market, Inc.

Form 10-Q

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Part 1. Financial Information

Item 1. Financial Statements

Whole Foods Market, Inc.

Condensed Consolidated Balance Sheets

April 11, 2004 (unaudited) and September 28, 2003

(In thousands)

Assets

The accompanying notes are an integral part of these condensed consolidated financial statements.

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Whole Foods Market, Inc.

Condensed Consolidated Income Statements (unaudited)

(In thousands, except per share amounts)

The accompanying notes are an integral part of these condensed consolidated financial statements.

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Whole Foods Market, Inc.

Condensed Consolidated Statements of Cash Flows (unaudited)

(In thousands)

The accompanying notes are an integral part of these condensed consolidated financial statements.

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Whole Foods Market, Inc.

Notes To Condensed Consolidated Financial Statements (unaudited)

April 11, 2004

(1) Basis of Presentation

The accompanying unaudited condensed consolidated financial statements of Whole Foods Market, Inc. (“Company”) have been prepared in accordance with generally accepted accounting principles for interim financial statements and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. In the opinion of management, the accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring accruals, considered necessary for a fair presentation. Preparing financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, expenses and related disclosures of contingent assets and liabilities. Examples include accounting for depreciation and amortization, inventory, allowance for doubtful accounts, long-term investments, team member benefit plans, team member health insurance plans, asset impairment charges, store closure costs, goodwill valuation, income taxes and contingencies. Actual results may differ from these estimates. Interim results are not necessarily indicative of results for any other interim period or for a full fiscal year. The information included in this Form 10-Q should be read in conjunction with Management’s Discussion and Analysis, the consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 28, 2003. Our fiscal year ends on the last Sunday in September. The first fiscal quarter is sixteen weeks, the second and third quarters each are twelve weeks and the fourth quarter is twelve or thirteen weeks. Where appropriate, we have reclassified prior year financial statements to conform to current year presentation. We operate in one reportable segment, natural food supermarkets. At April 11, 2004, we had one store in Canada and seven stores in the United Kingdom. All of our remaining operations are domestic.

(2) Restricted Cash

At April 11, 2004, we had approximately $18 million in restricted cash included in current assets on our Condensed Consolidated Balance Sheets. This amount primarily relates to cash held as collateral to support projected workers’ compensation obligations which previously were secured by letters of credit outstanding under our line of credit facility at September 28, 2003.

(3) Long-Term Investments

During the first quarter of fiscal year 2004, we sold all of our investments in unrestricted and restricted common shares of Gaiam, Inc. for approximately $1.8 million, resulting in a loss of approximately $0.5 million. During the first quarter of fiscal year 2003, our equity interest in Gaiam.com was converted into $1.0 million in cash and 250,000 restricted shares of Gaiam, Inc. common stock pursuant to the merger of a subsidiary of Gaiam, Inc. into Gaiam.com. Subsequent to this transaction, we recognized losses totaling approximately $1.4 million for other-than-temporary impairment of our unrestricted and restricted investments in Gaiam, Inc. common stock due to a sustained decline in market value of the stock below our carrying value. These losses have been included in “Investment and other income” on the accompanying Condensed Consolidated Income Statements in both fiscal years.

(4) Business Combinations

Select Fish LLC

On October 27, 2003, we acquired certain assets of Select Fish LLC (“Select Fish”) in exchange for approximately $3 million in cash plus the assumption of certain liabilities. The assets acquired are all assets relating to a seafood processing and distribution facility located in Seattle, Washington. This transaction was accounted for using the purchase method. Accordingly the purchase price has been allocated to tangible and identifiable intangible assets acquired based on their estimated fair values at the date of the acquisition. Total costs in excess of tangible and intangible assets acquired of approximately $1.1 million have been recorded as goodwill. Select Fish results of operations are included in our Condensed Consolidated Income Statements for the period beginning October 27, 2003 through April 11, 2004.

Fresh & Wild Holdings Limited

On January 31, 2004, we acquired all of the outstanding stock of Fresh & Wild Holdings Limited (“Fresh & Wild”) for a total of approximately $20 million in cash and approximately $16 million in Company common stock, totaling 238,735 shares. Fresh & Wild owned and operated seven natural and organic food stores in London and Bristol, England. This transaction was accounted for using the purchase method and, accordingly, the purchase price has been allocated on a preliminary basis to tangible and identifiable intangible assets acquired based on their estimated fair values at the date of acquisition. Total costs in excess of tangible and intangible assets acquired of approximately $30.4 million have been recorded as goodwill. The Company also agreed to an additional purchase price consideration contingent on the market price of Company common stock at January 31, 2006. If the market price of Company stock at January 31, 2006 is less than the market price at acquisition of $68.59 per share, those sellers who received and continuously hold through January 31, 2006 Company common stock are

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eligible to receive an amount, in stock, cash or any combination thereof, equal to the deficit multiplied by the number of shares continuously held. Fresh & Wild results of operations are included in our Condensed Consolidated Income Statements for the period beginning February 1, 2004 through March 31, 2004. John Mackey, our Chief Executive Officer and Walter Robb, our Co-Chief Operating Officer each owned approximately 0.2% of the outstanding stock of Fresh & Wild and received proceeds totaling approximately $54,000 and $78,000, respectively, as consideration for their ownership interest.

(5) Goodwill and Other Intangible Assets

Goodwill and indefinite-lived intangible assets are reviewed for impairment annually, or more frequently if impairment indicators arise. We allocate goodwill to one reporting unit for goodwill impairment testing. During the first and second quarters of fiscal year 2004, we acquired goodwill totaling approximately $31.5 million in connection with the acquisition of Select Fish and Fresh & Wild. There were no impairments of goodwill or indefinite-lived intangible assets during the twelve and twenty-eight week periods ended April 11, 2004.

All of our acquired identifiable intangible assets are subject to amortization. Amortization expense is recorded on a straight-line basis over the life of the related agreement, currently one to 26 years for contract-based intangible assets and one to five years for marketing-related and other identifiable intangible assets. During the first quarter of fiscal year 2004, we acquired intangible assets totaling approximately $0.2 million in connection with the Select Fish acquisition. During the second quarter of fiscal year 2004, we acquired intangible assets totaling approximately $0.3 million in connection with the Fresh & Wild acquisition. Amortization associated with intangible assets totaled approximately $0.7 million and $1.6 million for the twelve and twenty-eight weeks ended April 11, 2004, respectively and approximately $0.7 million and $1.6 million, respectively, for the same periods of the prior fiscal year. The components of intangible assets were as follows (in thousands):

Amortization associated with the net carrying amount of intangible assets at April 11, 2004 is estimated to be $1.7 million for the remainder of fiscal year 2004, $3.0 million in fiscal year 2005, $2.4 million in fiscal year 2006, $1.6 million in fiscal year 2007 and $1.4 million in fiscal year 2008.

(6) Earnings Per Share

The computation of basic earnings per share is based on the number of weighted average common shares outstanding during the period. The computation of diluted earnings per share includes the dilutive effect of common stock equivalents consisting of common shares deemed outstanding from the assumed exercise of stock options and the assumed conversion of zero coupon convertible subordinated debentures. A reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations follows (in thousands):

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The computations of diluted earnings per share for the twelve and twenty-eight week periods ended April 11, 2004 include all common stock equivalents. Options to purchase approximately 1,060,000 shares and 454,000 shares of common stock were not included in the computation of diluted earnings per share for the twelve and twenty-eight week periods ended April 13, 2003, respectively.

(7) Dividends

On March 22, 2004 the Company declared a cash dividend of $0.15 per share, for a total of approximately $9.3 million, to be paid April 19, 2004 to shareholders of record as of April 9, 2004. During the first quarter of fiscal year 2004 the Company declared and paid a cash dividend of $0.15 per share, for a total of approximately $9.1 million. The Company will pay future dividends at the discretion of our Board of Directors. The continuation of these payments and the amount of such dividends depend on many factors, including the results of operations and the financial condition of the Company. Subject to such factors, and a determination that cash dividends continue to be in the best interest of our shareholders, the current intention of our Board of Directors is to pay a quarterly dividend on an ongoing basis. During the first quarter of fiscal year 2004 we amended our bank credit agreement to allow for the payment of dividends on common stock.

(8) Comprehensive Income

Our comprehensive income was comprised of net income, unrealized gains and losses on marketable securities and foreign currency translation adjustment, net of income taxes. Comprehensive income, net of related tax effects, was as follows (in thousands):

(9) Stock-Based Compensation

The Company follows Accounting Principles Board Opinion (“APB”) No. 25, “Accounting for Stock Issued to Employees” and related interpretations in accounting for stock option grants. APB No. 25 provides that the compensation expense relative to our team member stock options is measured based on the intrinsic value of the stock option at the date of the grant. As required by Statement of Financial Accounting Standards (“SFAS”) No. 123 and SFAS No. 148, we have determined pro forma net income and pro forma net income per common share as if compensation costs had been determined based on the fair value of the options granted to team members and then recognized ratably over the vesting period. The fair value of stock option grants has been estimated at the date of grant using the Black-Scholes multiple option pricing model. Had we recognized compensation costs as prescribed by SFAS No. 123, net income, basic earnings per share and diluted earnings per share would have changed to the pro forma amounts shown below (in thousands, except per share data):

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The assumptions used to calculate the fair value of options granted are evaluated and revised, as necessary, to reflect market conditions and experience.

(10) Recent Accounting Pronouncements

The Financial Accounting Standards Board (“FASB”) issued FASB Interpretation (“FIN”) 46 and FIN 46-R, “Consolidation of Variable Interest Entities,” in April 2003 and December 2003, respectively. FIN 46 is effective immediately for variable interest entities (“VIEs”) created or acquired after April 31, 2003. FIN 46 and FIN 46-R shall be applied to VIEs in which an enterprise holds an interest it acquired before February 1, 2003 by the end of the first reporting period ending after March 15, 2004, the second quarter of fiscal year 2004 for the Company. The interpretations provide guidance related to identifying variable interest entities and determining whether such entities should be consolidated. Certain disclosures are required if it is reasonably possible that a company will consolidate or disclose information about a variable interest entity. The Company has no interest in a variable interest entity, and therefore the adoption of FIN 46 did not have any impact on our results of operations or financial condition. However, if the Company enters into any such arrangement with a variable interest entity in the future, the Company’s results of operations and financial condition could be impacted.

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

General

Whole Foods Market, Inc. owns and operates the country’s largest chain of natural and organic foods supermarkets. Our Company mission is to promote vitality and well-being for all individuals by supplying the highest quality, most wholesome foods available. Through our growth, we have had a large and positive impact on the natural and organic foods movement throughout the United States, helping lead the industry to nationwide acceptance. We opened our first store in Texas in 1980 and have expanded our operations to 156 stores as of April 11, 2004 both by opening new stores and acquiring existing stores from third parties. We operate in one reportable segment, natural and organic foods supermarkets. As of April 11, 2004 we had one store in Toronto, Ontario, Canada, and seven stores in the United Kingdom. All of our remaining operations are domestic. Our results of operations have been and may continue to be materially affected by the timing and number of new store openings. New stores generally become profitable during their first year of operation, although some new stores may incur operating losses for the first several years of operation. The Company reports its results of operations on a fifty-two or fifty-three week fiscal year ending on the last Sunday in September. The first fiscal quarter is sixteen weeks, the second and third quarters each are twelve weeks and the fourth quarter is twelve or thirteen weeks.

Results of Operations

The following table sets forth the Company’s income statements data expressed as a percentage of sales:

Figures may not add due to rounding.

Sales

Sales increased approximately 24% and 23% for the twelve and twenty-eight weeks ended April 11, 2004, respectively, compared to the same periods of the prior fiscal year. These increases were driven by comparable store sales growth of approximately 17.1% and 15.8%, respectively, and weighted average year-over-year square footage growth of approximately 7% and 8%, respectively. Sales of a store are deemed to be comparable commencing in the fifty-third full week after the store was opened or acquired. Sales in identical stores, which exclude relocated stores and major store expansions, increased approximately 17.0% and 15.5% for the twelve and twenty-eight weeks ended April 11, 2004, respectively. The Company believes its comparable store sales growth has been accelerating as natural and organic products enter the mainstream consciousness, and due to improvements in overall store execution and stronger brand awareness. We attribute our 17.1% comparable store sales growth in the second quarter primarily to these factors as well as a below-average 7.0% comparable stores sales increase for the same period of the prior fiscal year, and to the positive 70 basis point impact from United Food and Commercial Workers union strike in Southern California during the last fourteen weeks of our first quarter and the first six weeks of the second quarter. Nineteen of our stores experienced increased sales due to the strike, 18 of which are currently in the comparable store base.

Gross Profit

Gross profit consists of sales less cost of goods sold and occupancy costs plus contribution from non-retail distribution and food preparation operations. The Company’s gross profit as a percentage of sales for the twelve and twenty-eight weeks ended April 11, 2004 was approximately 35.5% and 34.9%, respectively, compared to approximately 34.5% and 34.2%, respectively, for the same periods of the prior fiscal year. This increase reflects lower occupancy costs and costs of goods sold as a percentage of sales, as well as improved contribution from non-retail facilities.

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Direct Store Expenses

Direct store expenses as a percentage of sales were approximately 25.4% and 25.3%, respectively, for the twelve and twenty-eight weeks ended April 11, 2004 compared to approximately 24.9% and 25.1%, respectively, for the same periods of the prior fiscal year. These increases were primarily due to increases in health care and benefit expenses, asset write-offs related to significant remodels, and professional and legal fees.

General and Administrative Expenses

General and administrative expenses as a percentage of sales were approximately 3.2% for the twelve and twenty-eight weeks ended April 11, 2004 compared to approximately 3.2% and 3.3%, respectively, for the same periods of the prior fiscal year. This Company maintains a continued focus on managing general and administrative expenses at both the regional and national levels.

Pre-opening and Relocation Costs

Pre-opening costs include costs associated with hiring and training personnel, supplies and certain occupancy and miscellaneous costs related to new locations and facilities internally developed. Relocation costs consist of moving costs, remaining lease payments, accelerated depreciation costs and other costs associated with replaced stores and facilities. Pre-opening and relocation costs associated with stores opened or stores under development were approximately $2.5 million and $4.3 million during the twelve and twenty-eight weeks ended April 11, 2004, respectively, and approximately $2.0 million and $5.8 million, respectively, for the same periods of the prior fiscal year. The number of stores and facilities opened and relocated were as follows:

The Company had 46 and 27 stores in development at May 4, 2004 and May 7, 2003, respectively.

Interest Expense

Interest expense consists of costs related to the convertible subordinated debentures, senior notes payable and bank line of credit, net of capitalized interest associated with new store development and internally-developed software. Net interest expense for the twelve and twenty-eight weeks ended April 11, 2004 totaled approximately $1.9 million and $4.3 million, respectively, compared to approximately $2.0 million and $4.6 million, respectively, for the same periods of the prior fiscal year. Capitalized interest for the twelve and twenty-eight weeks ended April 11, 2004 was approximately $0.4 million and $0.8 million, respectively, compared to approximately $0.3 million and $0.7 million, respectively, for the same periods of the prior fiscal year. No amounts were outstanding under the Company’s bank line of credit during fiscal years 2004 or 2003.

Investment and Other Income

Investment and other income consist primarily of interest income, rental income, investment gains and losses and other income. Investment and other income for the twelve and twenty-eight weeks ended April 11, 2004 totaled approximately $1.5 million and $3.0 million, respectively, compared to approximately $0.8 million and $0.1 million, respectively, for the same periods of the prior fiscal year. These increases are due primarily to an increase in balance of cash and cash equivalents. During the first quarter of fiscal year 2004, we sold all of our investments in unrestricted and restricted common shares of Gaiam, Inc. for approximately $1.8 million, resulting in a loss of approximately $0.5 million. During the first quarter of fiscal year 2003, the Company recognized a pre-tax impairment charge of approximately $1.4 million on our investments in Gaiam, Inc. due to a sustained decline in the market value of our investments below our carrying value.

Liquidity and Capital Resources and Changes in Financial Condition

We generated cash from operating activities of approximately $112.9 million and $197.4 million for the twelve and twenty-eight weeks ended April 11, 2004, respectively, compared to approximately $69.2 million and $140.1 million, respectively, in the same periods of the prior fiscal year. Cash flows from operating activities resulted primarily from our net income plus non-cash expenses, income tax benefits that resulted from the exercise of team member stock options and changes in operating working capital.

We have a $100 million revolving line of credit available through October 1, 2004. The credit agreement contains certain restrictive and affirmative covenants, including maintenance of certain financial ratios as defined in the agreement. We amended

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our bank credit agreement on November 12, 2003 to allow for the payment of dividends on common stock. All outstanding amounts borrowed under this agreement bear interest at our option of either a defined base rate or the LIBOR rate plus a premium. Commitment fees of 0.20% of the undrawn amount are payable under this agreement. At April 11, 2004, no amounts were drawn and the amount available was effectively reduced to approximately $91.3 million by approximately $8.7 million in outstanding letters of credit. At September 28, 2003, no amounts were drawn and the amount available was effectively reduced to approximately $80.2 million by approximately $19.8 million in outstanding letters of credit. In connection with the Fresh & Wild acquisition, we assumed a three-year revolving bank credit facility of approximately $5.3 million due June 1, 2004 on which approximately $4.2 million was drawn at April 11, 2004. The Company has outstanding zero coupon convertible subordinated debentures which had a carrying amount of approximately $155.3 million at April 11, 2004 and $151.4 million at September 28, 2003, respectively. The debentures have an effective yield to maturity of five percent and a principal amount at maturity on March 2, 2018 of approximately $308.3 million. The debentures are convertible at the option of the holder, at any time on or prior to maturity, unless previously redeemed or otherwise purchased. The debentures have a conversion rate of 10.640 shares per $1,000 principal amount at maturity, representing approximately 3,281,000 shares. As of April 11, 2004 approximately 500 debentures have been converted, at the option of the holder, to date into approximately 5,000 shares of Company common stock. The debentures may be redeemed at the option of the holder on March 2, 2008 or March 2, 2013 at the issue price plus accrued original discount totaling approximately $188 million or $241 million, respectively. At March 2, 2008 and March 2, 2013 the issue price plus accrued original discount will equal a conversion stock price of $57.36 and $73.42, respectively. Subject to certain limitations, at our option, we may elect to pay this purchase price in cash, shares of common stock or any combination thereof. The debentures may also be redeemed in cash at the option of the holder if there is a change in control at the issue price plus accrued original discount to the date of redemption. The Company has the option at any time, with 30 days notice, to redeem the debentures for cash, in whole or in part, at redemption prices equal to the issue price plus accrued original discount to the date of redemption. The debentures are subordinated in the right of payment to all existing and future senior indebtedness. We also had outstanding at April 11, 2004 and September 28, 2003 approximately $17.1 million of senior unsecured notes that bear interest at 7.29% payable quarterly. Principal on the senior notes is payable in annual installments of approximately $5.7 million through May 16, 2006. Net cash provided by financing activities was approximately $19.8 million and $22.6 million for the twelve and twenty-eight weeks ended April 11, 2004, respectively, as compared to approximately $24.2 million and $36.6 million, respectively, for the same periods of the prior fiscal year.

The following table shows payments due by period on contractual obligations as of April 11, 2004 (in thousands):

The following table shows expirations per period on commercial commitments as of April 11, 2004 (in thousands):

We periodically make other commitments and become subject to other contractual obligations that we believe to be routine in nature and incidental to the operation of the business. Management believes that such routine commitments and contractual obligations do not have a material impact on our business, financial condition or results of operations.

On March 22, 2004 the Company declared a cash dividend of $0.15 per share, for a total of approximately $9.3 million, to be paid April 19, 2004 to shareholders of record as of April 9, 2004. During the first quarter of fiscal year 2004 the Company declared and paid a cash dividend of $0.15 per share, for a total of approximately $9.1 million. The Company will pay future dividends at the discretion of our Board of Directors. The continuation of these payments and the amount of such dividends depend on many factors, including the results of operations and the financial condition of the Company. Subject to such factors, and a determination that cash dividends continue to be in the best interest of our shareholders, the current intention of our Board of Directors is to pay a quarterly dividend on an ongoing basis. We amended our bank credit agreement on November 12, 2003 to allow for the payment of dividends on common stock.

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Our principal historical capital requirements have been the funding of the development or acquisition of new stores and acquisition of property and equipment for existing stores. The required cash investment for new stores varies depending on the size of the new store, geographic location, degree of work performed by the landlord and complexity of site development issues. Over the past three fiscal years, our new store investment has averaged approximately $8.6 million per location. This excludes new store inventory of approximately $700,000, a portion of which is financed by our vendors. As of May 4, 2004, we had signed leases for 46 stores averaging approximately 46,400 square feet in size. During the second quarter of fiscal year 2004, we completed the acquisition of Fresh & Wild, which operated seven natural and organic food stores in London and Bristol, England, for approximately $20 million in cash and approximately $16 million in Company common stock. We will incur additional capital expenditures during the remainder of fiscal year 2004 in connection with ongoing equipment upgrades and resets at existing stores and continued development of management information systems. During the second quarter of fiscal year 2004, the Company loaned $13.5 million to a third-party real estate developer in connection with the construction of a new Company store. Net cash used in investing activities was approximately $101.0 million and $189.4 million for the twelve and twenty-eight weeks ended April 11, 2004, respectively, as compared to approximately $40.4 million and $95.5 million, respectively, for the same periods of the prior fiscal year. Absent any significant cash acquisition or change in status of the Company’s outstanding zero coupon convertible bond issue, we expect planned expansion and other anticipated working capital and capital expenditure requirements will be funded by cash generated from operations. We continually evaluate the need to establish other sources of working capital and will seek those considered appropriate based upon the Company’s needs and market conditions.

Critical Accounting Policies

The preparation of our financial statements in conformity with generally accepted accounting principles requires us to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, expenses and related disclosures of contingent assets and liabilities. Actual results may differ from these estimates. We base our estimates on historical experience and on various other assumptions and factors that we believe to be reasonable under the circumstances. On an ongoing basis, we evaluate the continued appropriateness of our accounting policies and resulting estimates to make adjustments we consider appropriate under the facts and circumstances.

We have chosen accounting policies that we believe are appropriate to report accurately and fairly our operating results and financial position, and we apply those accounting policies in a consistent manner. Our significant accounting policies are summarized in Note 2 of the consolidated financial statements included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 28, 2003. We believe that the following accounting policies are the most critical in the preparation of our financial statements because they involve the most difficult, subjective or complex judgments about the effect of matters that are inherently uncertain.

Insurance and Self-Insurance Reserves

The Company uses a combination of insurance and self-insurance plans to provide for the potential liabilities for workers’ compensation, general liability, property insurance, director and officers’ liability insurance, vehicle liability and employee health care benefits. Liabilities associated with the risks that are retained by the Company are estimated, in part, by considering historical claims experience, demographic factors, severity factors and other actuarial assumptions. While we believe that our assumptions are appropriate, the estimated accruals for these liabilities could be significantly affected if future occurrences if claims differ from these assumptions and historical trends.

Inventory Valuation

We value our inventories, both retail and wholesale, at the lower of cost or market. Cost is principally determined by the last-in, first-out (“LIFO”) method. LIFO cost was determined using the retail method for approximately 52% and 55% of inventories at April 11, 2004 and September 28, 2003, respectively, and was determined using the item cost method for approximately 43% and 42% of inventories at April 11, 2004 and September 28, 2003, respectively. The excess of estimated current costs over LIFO carrying value was approximately $10.9 million and $9.1 million at April 11, 2004 and September 28, 2003, respectively. Under the retail inventory method, the valuation of inventories at cost and the resulting gross margins are determined by applying a cost-to-retail ratio for various groupings of similar items to the retail value of inventories. Inherent in the retail inventory method calculations are certain management judgments and estimates, including shrinkage, which could impact the ending inventory valuation at cost as well as the resulting gross margins. Costs for the balance of inventories, are determined by the first-in, first-out (“FIFO”) or average cost method. We believe we have the appropriate inventory valuation controls in place to minimize the risk that inventory values would be materially misstated.

Goodwill and Intangible Assets

In July 2001, the Financial Accounting Standards Board (“FASB”) issued Statement of Financial Accounting Standards (“SFAS”) No. 142, “Goodwill and Other Intangible Assets.” Under SFAS No. 142, goodwill is no longer amortized but is

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reviewed for impairment on a reporting unit level annually, or more frequently if impairment indicators arise. We allocate goodwill to one reporting unit for goodwill impairment testing. We determine fair value utilizing both a market value method and discounted projected future cash flows compared to our carrying value for the purpose of identifying impairment. Our evaluation of goodwill and intangible assets with indefinite useful lives for impairment requires extensive use of accounting judgment and financial estimates. Application of alternative assumptions and definitions, such as reviewing goodwill for impairment at a different organizational level, could produce significantly different results.

Risk Factors

We wish to caution you that there are risks and uncertainties that could cause our actual results to be materially different from those indicated by forward-looking statements that we make from time to time in filings with the Securities and Exchange Commission, news releases, reports, proxy statements, registration statements and other written communications, as well as oral forward-looking statements made from time to time by representatives of our Company. These risks and uncertainties include, but are not limited to, those listed in the Company’s Annual Report on Form 10-K for the year ended September 28, 2003. These risks and uncertainties and additional risks and uncertainties not presently known to us or that we currently deem immaterial may cause our business, financial condition, operating results and cash flows to be materially adversely affected. Except for the historical information contained herein, the matters discussed in this analysis are forward looking statements that involve risks and uncertainties, including but not limited to general business conditions, the timely development and opening of new stores, the impact of competition, and other factors which are often beyond the control of the Company. The Company does not undertake any obligation to update forward-looking statements except as required by law.

Item 3. Quantitative and Qualitative Disclosures About Market Risk

Except as discussed below, there have been no material changes in the Company’s market risk exposures from those reported in our Annual Report on Form 10-K for the year ended September 28, 2003.

Market Risk

During the first quarter of fiscal year 2004, we sold all of our investments in unrestricted and restricted common shares of Gaiam, Inc. for approximately $1.8 million, resulting in a loss of approximately $0.5 million.

Item 4. Controls and Procedures

The Company maintains disclosure controls and procedures that are designed to ensure that information required to be disclosed in its reports filed pursuant to the Securities Exchange Act of 1934, as amended, is recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms, and that such information is accumulated and communicated to the Company’s management, including its Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. Management, with the participation of the Chief Executive Officer and Chief Financial Officer of the Company, has performed an evaluation of the design and operation of the Company’s disclosure controls and procedures as of the end of the period covered by this Report. Based on that evaluation, the Chief Executive Officer and Chief Financial Officer of the Company concluded that the Company’s disclosure controls and procedures were effective as of the end of the period covered by this Report.

Management, with the participation of the Chief Executive Officer and Chief Financial Officer of the Company, has evaluated any changes in the Company’s internal control over financial reporting that occurred during the most recent fiscal quarter. Based on that evaluation, management, the Chief Executive Officer and the Chief Financial Officer of the Company have concluded that there has been no change in the Company’s internal control over financial reporting during the most recent fiscal quarter that has materially affected, or is reasonably likely to materially affect, the Company’s internal control over financial reporting.

Part II. Other Information

Item 1. Legal Proceedings

The Company is subject to various legal proceedings and claims arising in the ordinary course of business. The Company’s management does not expect that the outcome in the current proceedings, individually or collectively, will have a material adverse effect on the Company’s financial condition, operating results or cash flows.

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

On January 30, 2004, we issued 238,735 shares of Company common stock with market value of approximately $16.4 million as partial consideration in connection with the acquisition all of the outstanding stock of Fresh & Wild. These securities were offered and sold without registration under the Securities Act in reliance upon the exemption provided by Section 4(2). The resale of these shares was subsequently registered under the Securities Act pursuant to a registration statement (File No. 333-113476) which became effective on March 19, 2004.

Item 4. Submission of Matters to Vote of Security Holders

On March 22, 2004, the Company held its annual meeting of shareholders at which shareholders:

Voting results were as follows:

Item 6(a). Exhibits

Item 6(b). Reports on Form 8-K

The Company furnished a report on Form 8-K dated February 11, 2004 regarding the announcement of the results of operations for the fiscal quarter ended January 18, 2004.

The Company filed a report on Form 8-K dated March 22, 2004 announcing that its Board of Directors had declared a dividend of $0.15 per share, payable April 19, 2004 to shareholders of record as of April 9, 2004.

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SIGNATURE

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.

Whole Foods Market, Inc.

Registrant

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