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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

For the quarterly period ended July 3, 2004

or

For the transition period from              to             

Commission File Number 001-09781 (0-1052)

MILLIPORE CORPORATION

(Exact name of registrant as specified in its charter)

(978) 715-4321

(Registrant’s telephone number, 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  x    No  ¨

Indicate by check mark whether the registrant is an accelerated filer (as defined in Exchange Act

Rule 12b-2).    Yes  x    No  ¨

As of July 23, 2004, there were 49,581,464 shares of the registrant’s Common Stock outstanding.

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MILLIPORE CORPORATION

INDEX TO FORM 10-Q

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MILLIPORE CORPORATION

CONDENSED CONSOLIDATED BALANCE SHEETS

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

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MILLIPORE CORPORATION

CONDENSED CONSOLIDATED STATEMENTS OF INCOME

(In thousands, except per share data)

(Unaudited)

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

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MILLIPORE CORPORATION

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

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

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(In thousands, except per share data)

1. General

Millipore Corporation (“Millipore”, “our” or “we”) is a multinational bioscience company that provides technologies, tools and services for the discovery, development and production of therapeutic drugs and for other purposes. We serve customers in the worldwide biotechnology, life science research and other bioscience markets with a variety of products and services used in the purification, separation and analysis of fluids. Our products are based on a variety of enabling technologies, including membrane filtration and chromatography.

A variety of our products are used in the biotechnology market by biotechnology and pharmaceutical companies that manufacture therapeutic products based on recombinant proteins. A number of our products are used by our customers in the life science research market for drug discovery and drug development. A range of our products have general applications in the other bioscience market in non-biological pharmaceutical manufacturing, clinical and analytical laboratories, environmental monitoring and quality control.

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with the instructions to Form 10-Q and, accordingly, these footnotes condense or omit information and disclosures which substantially duplicate information provided in our latest audited financial statements. These financial statements should be read in conjunction with the financial statements and notes included in our Annual Report on Form 10-K for the year ended December 31, 2003.

Certain reclassifications have been made to prior year’s financial statements to conform to the 2004 presentation.

Our interim fiscal quarter typically ends on the thirteenth Saturday of each quarter. Since our fiscal year-end is December 31, the first and fourth fiscal quarters may not consist of thirteen complete weeks. The second fiscal quarters for 2004 and 2003 ended on July 3, 2004 and June 28, 2003, respectively.

In the opinion of our management, these financial statements reflect all adjustments necessary for a fair presentation of the results for the interim periods presented. The accompanying unaudited condensed consolidated financial statements are not necessarily indicative of future trends or our operations for the entire year.

2. Stock-based Compensation

At July 3, 2004, we have a stock-based employee compensation plan and a non-employee director stock option plan from which we currently grant stock options. We apply the recognition and measurement provisions of Accounting Principles Board Opinion No. 25 (“APB 25”), “Accounting for Stock Issued to Employees,” and related interpretations in accounting for those plans. Stock-based employee compensation expense was recorded in net income during the quarter ended July 3, 2004 in relation to the CEO separation agreement. Stock-based employee compensation expense related to vesting of shares of restricted stock is reflected in net income. These shares of restricted stock were granted at no cost to employees in prior years.

The following table illustrates the effect on net income and earnings per share as if we had applied the fair value recognition provisions of Statement of Financial Accounting Standards (“SFAS”) No. 123, “Accounting for Stock-based Compensation,” to stock-based employee compensation for the three and six months ended July 3, 2004 and June 28, 2003.

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS – (Continued)

(In thousands, except per share data)

The fair value of each option grant is estimated on the date of the grant using the Black-Scholes model. The assumptions used in the Black-Scholes calculation for the three and six months ended July 3, 2004 and June 28, 2003 included an expected life of five years, a dividend rate of zero, expected volatility of 40%, and weighted average risk-free interest rates of 3.0% for the three and six months ended July 3, 2004 and 4.2% for the three and six months ended June 28, 2003.

3. Inventories

Inventories at July 3, 2004 and December 31, 2003, stated at the lower of first-in, first-out (“FIFO”) cost or market, consisted of the following:

4. Property, Plant and Equipment

Accumulated depreciation on property, plant and equipment was $238,021 at July 3, 2004 and $222,911 at December 31, 2003.

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS – (Continued)

(In thousands, except per share data)

5. Intangible Assets, net

Intangible assets consisted of the following at July 3, 2004 and December 31, 2003:

Amortization expense for the six months ended July 3, 2004 and June 28, 2003 was $1,647 and $1,690, respectively.

The estimated aggregate amortization expense for intangible assets owned as of July 3, 2004 for each of the five succeeding years is as follows:

6. Notes Payable

We repaid the $75,000 7.23% note upon maturity on March 4, 2004.

7. Employee Retirement Plans

The following tables summarize the funded status of the U.S. Employee Retirement Plans at July 3, 2004 and June 28, 2003, based on SFAS No. 132 (revised 2003), “Employers’ Disclosures about Pensions and Other Postretirement Benefits.”

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS – (Continued)

(In thousands, except per share data)

As we previously disclosed in our financial statements for the year ended December 31, 2003, we expect to contribute $932 to our U.S. pension plan and $481 to our other post-retirement medical and life insurance plan in 2004. As of July 3, 2004, $394 of contributions have been made to our U.S. pension plan and $243 of contributions have been made to our post-retirement medical and life insurance plan.

8. Basic and Diluted Earnings per Share

The following table presents share information used to calculate earnings per share (“EPS”):

For the three months ended July 3, 2004 and June 28, 2003, outstanding stock options of 1,751 and 2,895, respectively, with purchase prices in excess of the Company’s average common stock fair value for the related period, were excluded from the calculation of diluted earnings per share because their inclusion would have been antidilutive. For the six months ended July 3, 2004 and June 28, 2003, outstanding stock options of 2,690 and 3,051, respectively, with purchase price in excess of the Company’s average common stock fair value for the related period, were excluded from the calculation of diluted earnings per share because their inclusion would have been antidilutive. Antidilutive options could become dilutive in the future.

9. Comprehensive Income

The following table presents the components of comprehensive income, net of taxes:

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS – (Continued)

(In thousands, except per share data)

10. Commitments and Contingencies

During the first quarter of 2004, we entered into new long-term supply agreements with two of our vendors. These vendors supply us with certain of our critical raw materials. Both of these supply agreements expire in 2008. These supply agreements require us to purchase a minimum of $10,417 during the period of July 3, 2004 through December 31, 2008.

Also during the first quarter of 2004, issues arose under our tax sharing agreement relating to the inclusion of Mykrolis Corporation (“Mykrolis”), our former subsidiary, in our consolidated tax return for portions of 2001 and 2002. We have made a payment to Mykrolis of $1,255 with respect to these issues. Mykrolis has questioned whether this amount is sufficient to resolve the issues. We are investigating the matter and expect a resolution by year end. As part of that resolution there could be an additional obligation owing to Mykrolis.

11. Transactions with Related Parties and Affiliates

On April 28, 2004, Francis J. Lunger announced that he will be stepping down as President and CEO of Millipore when his replacement has been named but before March 1, 2005. In connection with Mr. Lunger’s separation agreement, we expect to record expense of approximately $3,000 relating to severance, bonus and related benefits which will be recognized over his remaining service period. We also expect to record additional compensation expense of approximately $2,000 to $7,000 relating to stock options, of which approximately $2,000 will be recorded over his remaining service period and the remainder will be recorded upon his separation. The amount of expense, within the above range relating to stock options, will depend upon the timing of the exercise of his stock options. We accrued a total of $1,300 during the second quarter related to this separation agreement.

12. New Accounting Pronouncements

In January 2004, the Financial Accounting Standards Board (“FASB”) issued FASB Staff Position (“FSP”) No. 106-1, “Accounting and Disclosure Requirements Related to the Medicare Prescription Drug, Improvement and Modernization Act of 2003” (the “Act”). The Act introduces a prescription drug benefit under Medicare as well as a federal subsidy to sponsors of retiree health care benefit plans that provide a benefit that is at least actuarially equivalent to Medicare Part D. FSP No. 106-1 is effective for interim or annual financial statements of fiscal years ending after December 7, 2003. We have elected to defer the accounting for the Act until authoritative guidance on the accounting for the federal subsidy is issued and are assessing the impact.

In January 2003, FASB issued FASB Interpretation No. 46, “Consolidation of Variable Interest Entities” (“FIN 46”). This interpretation requires existing unconsolidated variable interest entities to be consolidated by their primary beneficiaries if the entities do not effectively disperse risks among the parties involved. It explains how to identify variable interest entities and how an enterprise assesses its interest in a variable interest entity to decide whether to consolidate that entity. In December 2003, the FASB issued Interpretation No. 46 (revised December 2003), “Consolidation of Variable Interest Entities,” (“FIN 46R”). FIN 46R replaces FIN 46 and revised the implementation date to the first fiscal year or interim period ending after March 15, 2004, with respect to variable interest entities in which an enterprise holds a variable interest that it acquired before February 1, 2003. The adoption of FIN 46R did not have an impact on our condensed consolidated financial statements.

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

Basis of Presentation

In this Form 10-Q, unless the context otherwise requires, the terms “Millipore”, “our”, “us” and “we” shall mean Millipore Corporation and its subsidiaries.

The following Management’s Discussion and Analysis of Financial Condition and Results of Operations should be read in conjunction with our Condensed Consolidated Financial Statements and related notes thereto and other financial information included elsewhere in this Form 10-Q and our Annual Report on Form 10-K for the year ended December 31, 2003. Throughout this discussion, reference will be made to “constant currencies”, previously referred to as “local currencies” in our Annual Report on Form 10-K for the year ended December 31, 2003. Constant currency results represent the foreign currency balances translated to U.S. dollars, in all periods presented, at Millipore’s predetermined budgeted exchange rates for 2004, thus excluding the impact of fluctuations in the actual foreign currency rates. In addition to analyzing financial results at actual rates of exchange, management uses this presentation because we believe that the constant currency results provide a clearer presentation of underlying business trends separate from the impact of foreign currency. The U.S. dollar results represent the foreign currency balances translated at actual exchange rates. Our interim fiscal quarter typically ends on the thirteenth Saturday of each quarter. Since our fiscal year-end is December 31, the first and fourth fiscal quarters may not consist of thirteen complete weeks. The second fiscal quarters for 2004 and 2003 ended on July 3, 2004 and June 28, 2003, respectively.

Executive Summary

During the three months ended July 3, 2004 (the “second quarter of 2004”) as compared with the three months ended June 28, 2003 (the “second quarter of 2003”), sales growth was 14.4% comprised of 11.0% growth in constant currencies and a 3.4% foreign currency impact. In the second quarter of 2004, we realized sales growth in all three of the markets that we serve, biotechnology, life science research and other bioscience. The increase in sales was due to improving worldwide economies that increased laboratory research spending as well as increased demand for our products by biotechnology customers. Operating income as a percent of sales was 17.1% in the second quarter of 2004 as compared with 16.6% in the second quarter of 2003. The primary reason for the increase in profitability during the second quarter of 2004 was that operating expenses grew at a slower rate than our sales as we continued to leverage our worldwide infrastructure. The increased profitability combined with on-going programs to control working capital resulted in strong operating cash flow that continues to be invested in increased productive capacity and debt reduction. The business dynamics for the six month period ended July 3, 2004 were similar to those in the second quarter of 2004. However, we expect the sales growth in the second half of 2004 to be less than the sales growth in the first half of 2004, although the amount can not be determined at this time.

Critical Accounting Policies and Estimates

This discussion and analysis of our financial condition and results of operations are based upon our condensed consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States of America. Our most critical accounting policies had a significant impact on the preparation of these condensed consolidated financial statements. These policies include estimates and significant judgments that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. We continue to have the same critical accounting policies and estimates as we described in Item 7, on page 14, in our Annual Report on Form 10-K for the year ended December 31, 2003. Those policies and estimates were identified as those relating to revenue recognition, allowance for doubtful accounts, inventory valuation analysis, valuation of long-lived assets, income tax provision, employee retirement plans and our intention to refinance short-term debt on a long-term basis. We continue to evaluate our estimates and judgments on an on-going basis. By their nature, these estimates and judgments are subject to an inherent degree of uncertainty. We base our estimates and judgments on historical experience and on various other assumptions that are believed to be reasonable under the circumstances. Actual results may differ materially from these estimates under different assumptions or conditions.

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Results of Operations

Second Quarter of 2004 Compared to the Second Quarter of 2003

Net Sales

The following discussion of net sales summarizes sales growth by the markets in which our products were used, by the geographies in which our products were sold, and by product types.

Net Sales by Market

We sell our products into the biotechnology, life science research and other bioscience markets. Net sales growth (second quarter of 2004 as compared with the second quarter of 2003) by market, is summarized in the table below.

Constant currency sales growth of 20.7% in the biotechnology market during the second quarter of 2004 as compared with the second quarter of 2003 was primarily due to a 24% growth in consumables sales driven principally by chromatography media sales. This demand was a result of increased manufacturing campaigns of marketed biotechnology drugs, as well as the start-up and validation of new customer production lines and their processes. Hardware sales to biotechnology customers grew approximately 5%. Sales of hardware can fluctuate significantly as they are driven by customer timing for capacity expansion.

Constant currency sales growth was 8.9% in the life science research market during the second quarter of 2004 as compared with the second quarter of 2003, primarily due to increased sales of consumables. This market is sensitive to worldwide economic conditions as well as life science research funding in both public and private institutions. The continued improvement of those conditions in the second quarter of 2004 as compared with the second quarter of 2003 contributed to the strong growth of the laboratory supply market particularly in the United States. Further, the economy, capital markets and private equity environment in the U.S. have improved thereby strengthening demand for life science research tools. In addition, we saw an increase in pharmaceutical research and development spending in all regions. Finally, bio-defense related research continues to grow especially in the United States.

Constant currency sales growth of 5.3% in the other bioscience market during the second quarter of 2004 as compared with the second quarter of 2003 was primarily due to increased sales of our consumables and laboratory water purification instruments. These products are used in basic research, clinics, microbial monitoring as well as testing, environmental, chemical and biological applications. Our laboratory water products continued to have strong growth driven by the introduction of new products, the build out of new laboratories, and the general increase in spending by pharmaceutical customers.

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Net Sales by Geography

Sales growth by geography for the second quarter of 2004 as compared with the second quarter of 2003 is summarized in the table below.

The U.S., which comprises over 90% of the total Americas, achieved sales growth of 15.1% during the second quarter of 2004 as compared to the second quarter of 2003, driven by strong sales of chromatography media consumables to our large biotechnology customers. In addition, U.S. sales of life science research consumables benefited as biotechnology and pharmaceutical customers increased spending on drug discovery research projects. Improving economies in the U.S. also helped stimulate growth in private and publicly funded laboratories. The increase in sales, in constant currencies, to customers in Europe was due to a slowly improving European economy and increased laboratory activities by customers within the other bioscience market in environmental, public health, clinical and university sectors. The increase in sales within the Asia/Pacific region was primarily due to increased government funding of biotechnology research initiatives in Japan and increased spending by pharmaceutical customers throughout the region. However, partially offsetting this growth was the impact of privatization of universities in Japan which spurred tighter control over research spending.

During the second quarter of 2004, the U.S. dollar remained weaker on average as compared to prior year levels. A weaker U.S. dollar positively impacts U.S. dollar sales growth. The impact of translating foreign currency sales to the U.S. dollar improved the reported sales growth rate by approximately 340 basis points in the second quarter of 2004. Since we have a higher percentage of our sales in Europe than Asia, the impact of translating sales denominated in European currencies will have a greater impact on our sales than the impact of translating sales denominated in Asian currencies.

The U.S. dollar weakened against the Euro on average by approximately 6% and against the Japanese Yen by approximately 8% during the second quarter of 2004 as compared with the second quarter of 2003.

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Net Sales by Product Type

Net sales growth by product type, for the second quarter of 2004 as compared with the second quarter of 2003, is summarized in the table below.

Our mix of revenue by product type has stayed relatively consistent over the last several quarters. Sales of our consumables remained strong as large biotechnology customers continued to purchase chromatography media for drug manufacturing campaigns or start-up and validation of new processes and production lines. Sales of hardware products grew 8.2%, as sales of laboratory instruments used in the life science research and other bioscience markets grew 9.7% compared with a 2.9% growth in sales of process scale hardware principally in the biotechnology market. The growth in the sales of services in the second quarter of 2004 was achieved across all markets. This increase is due to service revenues associated with the installed base of water filtration systems as well as increased support services to our other bioscience customers.

Gross Profit Margins

Gross profit margin percentages were 54.0% in the second quarter of 2004 as compared with 54.9% in the second quarter of 2003. The decrease in our gross profit margin percentage for the second quarter of 2004 as compared with the second quarter of 2003 was primarily due to the strengthening of the Euro and the British Pound against the U.S. dollar which increased the average cost of products manufactured in our European plants. Increased sales volumes favorably impacted production efficiencies in the second quarter of 2004. This was offset by a higher mix of chromatography media consumable products which have lower margins than filtration consumables.

Operating Expenses

Selling, general and administrative (“SG&A”) expenses increased $5.2 million, or 8.4%, in the second quarter of 2004 as compared with the second quarter of 2003. The increase during the second quarter of 2004 was primarily related to $2.8 million of unfavorable foreign exchange translation and $1.3 million for incremental compensation cost for the CEO. During the second quarter of 2004, Francis J. Lunger announced that he would be stepping down as President and CEO of Millipore when his replacement has been named but before March 1, 2005. In connection with Mr. Lunger’s separation agreement, we accrued $1.3 million which related to severance, bonus, stock options and related benefits. In addition, $0.4 million was spent during the quarter to recruit a replacement for Mr. Lunger. As a percentage of sales, SG&A expenses decreased from 31.5% to 29.8%.

Research and development (“R&D”) expenses increased $2.0 million, or 14.0%, in the second quarter of 2004 as compared with the second quarter of 2003. The increase during the second quarter of 2004 was due to continued investment in the level of research and development programs aimed at introducing new products to our markets and $0.5 million of unfavorable foreign exchange translation. As a percentage of sales, R&D expenses decreased from 7.2% to 7.1%.

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Restructuring and Other

During the second quarter of 2003, we completed the restructuring program that we had initiated during 2001 and recovered approximately $250 in assets that we had originally written-off and deemed uncollectible. Upon completion of this restructuring program, we reversed $604 of the original $17,962 estimated reserve which included the $250 recovered during this quarter and $354 of previously estimated lease and severance payments, as these amounts were no longer required.

Net Interest Expense

Net interest expense decreased $1.9 million in the second quarter of 2004 as compared with the second quarter of 2003. The lower net interest expense was principally a result of lower average debt outstanding. On March 4, 2004, we repaid our 7.23% $75.0 million debt with cash. During the second quarter of 2004, the weighted average interest rate on our revolving credit agreement was approximately 2.2%.

Provision for Income Taxes

Our effective tax rate on net income for the second quarter of 2004 was 22.0% as compared with 22.5% during the second quarter of 2003. The effective annual tax rate for 2004 is now expected to be 22.5% which is lower than the 23.0% effective annual tax rate expected in the first quarter of 2004. The decline in the estimated effective annual tax rate is due to an increase in the expected mix of profits from lower tax rate jurisdictions as compared to the first quarter of 2004.

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Six months ended July 3, 2004 compared to the six months ended June 28, 2003

Net Sales

The following discussion of net sales summarizes sales growth by the markets in which our products were used, by the geographies in which our products were sold, and by product types.

Net Sales by Market

We sell our products into the biotechnology, life science research and other bioscience markets. Net sales growth by market for the six months ended July 3, 2004 as compared with the six months ended June 28, 2003 is summarized in the table below.