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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

For the quarterly period ended October 2, 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 October 22, 2004, there were 49,730,078 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

(In thousands)

(Unaudited)

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

(In thousands)

(Unaudited)

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 precisely thirteen weeks. The third fiscal quarters for 2004 and 2003 ended on October 2, 2004 and September 27, 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 October 2, 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 recognized as an expense during the quarter ended October 2, 2004 in relation to the CEO separation agreement. Stock-based employee compensation expense related to vesting of shares of restricted stock is recognized as an expense. These shares of restricted stock were granted at no cost to employees in prior years.

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MILLIPORE CORPORATION

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS – (Continued)

(In thousands, except per share data)

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 nine months ended October 2, 2004 and September 27, 2003.

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 nine months ended October 2, 2004 and September 27, 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 3.5% and 3.1% for the three and nine months ended October 2, 2004, respectively, and 4.2% for the three and nine months ended September 27, 2003.

3. Inventories

Inventories at October 2, 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 $247,863 at October 2, 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 October 2, 2004 and December 31, 2003:

Amortization expense for the nine months ended October 2, 2004 and September 27, 2003 was $2,507 and $2,550, respectively.

The estimated aggregate amortization expense for intangible assets owned as of October 2, 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 October 2, 2004 and September 27, 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)

We expect to contribute $1,005 to our U.S. pension plan and $481 to our other post-retirement medical and life insurance plan in 2004. As of October 2, 2004, $780 of contributions have been made to our U.S. pension plan and $380 of contributions have been made to our post-retirement medical and life insurance plan.

We sponsor various non-U.S. retirement plans. The accrued pension cost for these plans is included in other long-term liabilities in the consolidated balance sheets. We expect to record pension costs related to our German plan totaling $1,560 for the full year of 2004 of which $1,061 was recorded in the third quarter of 2004.

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 October 2, 2004 and September 27, 2003, outstanding stock options of 2,953 and 1,817, respectively, with purchase prices in excess of our 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 nine months ended October 2, 2004 and September 27, 2003, outstanding stock options of 2,777 and 2,889, respectively, with purchase prices in excess of our 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:

For the quarter ended October 2, 2004, we recorded a minimum pension liability of $917 in the United Kingdom, as required by SFAS No. 87. The adjustment is reflected in other comprehensive income and other long-term liabilities.

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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 $9,830 during the period of October 2, 2004 through December 31, 2008.

Also during the first quarter of 2004, an issue 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. The agreement provides that if Millipore receives a tax benefit (as defined in the agreement) due to the inclusion of Mykrolis, Millipore is required to pay Mykrolis the amount of that benefit. During the first quarter of 2004, we made a payment to Mykrolis of $1,255 pursuant to the tax sharing agreement. Mykrolis has questioned the sufficiency of the payment.

11. Investment in Unconsolidated Affiliates

Our investments in two affiliated companies are accounted for using the equity method. We recorded $1,375 of undistributed earnings during the first nine months of 2004, all of which was recorded in the third quarter of 2004, and we received dividends from these unconsolidated affiliates totaling $394 during the first nine months of 2004. During the first nine months of 2003, we recorded $270 of undistributed earnings and we received dividends from these unconsolidated affiliates totaling $253.

12. Transactions with Related Parties

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 appointed 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 $4,000 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 have accrued a total of $2,686 for the nine months ended October 2, 2004 related to this separation agreement.

13. Subsequent Events

On October 25, 2004, we announced that Dr. Martin D. Madaus had been appointed President and CEO of Millipore, effective no later than February 1, 2005. He will also be joining the Board of Directors.

On October 22, 2004, President Bush signed the American Jobs Creation Act of 2004 (the “AJCA”) into law. The AJCA contains a number of provisions which will affect Millipore in the future. We will be reviewing the AJCA over the next few months in order to determine its impact on Millipore.

14. New Accounting Pronouncements

In January 2004, the FASB issued FASB Staff Position (“FSP”) No. 106-1 and in May 2004 issued FSP No. 106-2, “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 and FSP No. 106-2 is effective for interim or annual financial statements of fiscal years ending after June 15, 2004. 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.

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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 precisely thirteen weeks. The third fiscal quarters for 2004 and 2003 ended on October 2, 2004 and September 27, 2003, respectively.

Executive Summary

During the three months ended October 2, 2004 (the “third quarter of 2004”) as compared with the three months ended September 27, 2003 (the “third quarter of 2003”), sales growth was 5%, comprised of 1% growth in constant currencies and a 4% foreign currency impact. In the third quarter of 2004, sales to the biotechnology market declined 1% in constant currencies. The decline was primarily due to a single $6.4 million shipment in constant currencies ($7.2 million at actual rates of exchange) of chromatography media to a European customer during the third quarter of 2003. In the life science research market our sales grew 7%. Growth in this market was principally a result of strength in North American pharmaceutical spending in drug discovery and drug development and partially offset by weakness in government and university spending in Europe and Japan. In the third quarter of 2004, sales to the other biosciences market grew 1% as compared with the third quarter of 2003 due primarily to flat sales of consumables used in the production of small and large volume parenteral drugs and nutritional products.

Operating income as a percent of sales was 16.2% in the third quarter of 2004 as compared with 17.6% in the third quarter of 2003. The third quarter of 2003 included a $0.8 million gain on the sale of real estate. Selling, general and administrative (“SG&A”) increased 6.6% in the third quarter of 2004 as compared with the prior year. The current quarter included $1.3 million of expenses related to CEO accrued severance costs. Research and development (“R&D”) expenses grew 8.0% as we continued to invest in new product development programs as planned. Cash flows from operations increased to $107.9 million, a $19.6 million improvement for the nine months of 2004 as compared to the nine months of 2003, as a result of increased net income combined with on-going programs to control working capital. We continue to invest in productive capacity and to reduce our debt.

During the nine months ended October 2, 2004 as compared with the nine months ended September 27, 2003, our sales growth was 13% comprised of 7% growth in constant currencies and a 6% foreign currency impact. Sales growth in the third quarter of 2004 was lower than the sales growth in the first half of 2004 where we achieved 16% growth comprised of 11% constant currency growth and 5% foreign currency impact. The major sources of growth, in constant currencies, for the first nine months of 2004 were in the biotechnology and life science research markets which grew 11% and 9%, respectively. In the biotechnology market, sales of process scale filtration and chromatography media were particularly strong driven by increased manufacturing campaigns of marketed biotechnology drugs, and start-up and validation of new customer production lines and their processes. In the life science research market, sales growth was favorably impacted by drug discovery and drug development spending, especially in the United States. Operating income as a percent of sales was 16.8% in the first nine months of 2004 as compared with 17.0% in the first nine months of 2003. The decline in profitability as a percent of sales was due principally to unfavorable foreign exchange related to products manufactured in Europe and higher depreciation charges related to our expansion and upgrade of existing manufacturing capacity.

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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.

Results of Operations

Third Quarter of 2004 Compared to the Third 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 (third quarter of 2004 as compared with the third quarter of 2003) by market, is summarized in the table below.

In the biotechnology market, constant currency sales declined 1% during the third quarter of 2004 as compared with the third quarter of 2003 consisting of a 3% growth in consumables sales offset by a 15% decline in hardware sales. The biotechnology consumable sales growth rate of 3% in the third quarter of 2004 compares to the 21% sales growth of consumables in the first half of 2004, as compared to 2003. The decline was primarily due to a single $6.4 million shipment in constant currencies ($7.2 million at actual rates of exchange) of chromatography media to a European customer during the third quarter of 2003. Sales of hardware to biotechnology customers can fluctuate significantly as they are driven by customer timing for capacity expansion.

In the life science research market, constant currency sales grew 7% during the third quarter of 2004 as compared with the third quarter of 2003. This is primarily the result of a stronger economic climate in North America supporting growth in

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pharmaceutical spending for drug discovery and drug development, and a healthy research and government funding environment, especially for consumable supplies. In the life science research market, European growth was uneven as business reorganizations occurred at several large pharmaceutical customers. In addition, the French and German research market was sluggish with limited government funding. In Japan, we saw a decline in spending by university and other research laboratories related to changes in the government funding policies.

In the other bioscience market, constant currency sales grew 1% during the third quarter of 2004 as compared with the third quarter of 2003. This is primarily due to flat sales of consumables used in the production of small and large volume parenteral drugs and nutritional products.

Net Sales by Geography

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

The Americas achieved constant currency sales growth of 6%, driven by strong sales of process scale sterilizing consumable cartridges to our pharmaceutical and biotechnology customers. In addition, U.S. sales of life science research consumables benefited as pharmaceutical customers increased spending for drug discovery and research projects. The improving economy in the U.S. also helped stimulate growth in both private and publicly funded laboratories. In Europe, the 6% decline in customer sales, in constant currencies, was primarily due to a single $6.4 million shipment in constant currencies ($7.2 million at actual rates of exchange) of chromatography media to a biotechnology customer during the third quarter of 2003. While sales of laboratory water purification instruments and consumables, in general, remained strong in the European market, sales to government sponsored research laboratories in France and Germany slowed because of funding constraints. In addition, sales to large pharmaceutical customers in France have been sluggish due to several corporate reorganizations in progress. The growth in the Asia/Pacific region remained modest, particularly in the life science market as the Japanese government and universities adapted to new government policies involving the administration and utilization of research grants.

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During the third quarter of 2004, the U.S. dollar remained weaker on average as compared to the prior year. A weaker U.S. dollar positively impacts U.S. dollar sales growth because approximately 60% of our revenue is outside the U.S. The impact of translating foreign currency sales to the U.S. dollar improved the reported sales growth rate by approximately 410 basis points in the third 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 U.S. dollar sales than the impact of translating sales denominated in Asian currencies. The U.S. dollar weakened against the Euro on average by approximately 8% and against the Japanese Yen by approximately 7% during the third quarter of 2004 as compared with the third quarter of 2003.

Net Sales by Product Type

Net sales growth by product type, for the third quarter of 2004 as compared with the third 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. The growth rate of our consumables weakened to 2% as the third quarter of 2003 included a single $6.4 million shipment in constant currencies ($7.2 million at actual rates of exchange) of chromatography media to a biotechnology customer during the third quarter of 2003. Sales of hardware products declined 3%, primarily due to a 15% decline in sales of process scale hardware used principally in the biotechnology market. Sales of hardware can fluctuate significantly as they are driven by customer timing for capacity expansion. The growth in service revenues in the third quarter of 2004 was achieved across all markets.

Gross Profit Margins

Gross profit margin percentages were 53.8% in the third quarter of 2004 as compared with 54.2% in the third quarter of 2003. The decrease in our gross profit margin percentage for the third quarter of 2004 as compared with the third quarter of 2003 was primarily due to underutilized manufacturing capacity and higher depreciation expense. Over the past year we have focused on expanding and upgrading our production facilities as we prepare to meet the future needs of our customers. In addition, the decline in profit margin is the result of the Euro and the British Pound strengthening against the U.S. dollar, which increases the average cost of products manufactured in our European plants.

Operating Expenses

SG&A expenses increased $4.0 million, or 6.6%, in the third quarter of 2004 as compared with the third quarter of 2003. As a percentage of sales, SG&A expenses increased from 30.0% to 30.4%. The increase during the third quarter of 2004 was the result of $2.0 million of unfavorable foreign exchange translation, $1.1 million incremental pension expense for our German pension plan, and $1.3 million for incremental compensation cost for the CEO transition. These SG&A increases were partially offset by the $1.4 million of undistributed earnings recorded for our investments in two affiliated companies during the third quarter of 2004.

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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 appointed 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 during the third quarter of 2004.

R&D expenses increased $1.1 million, or 8.0%, in the third quarter of 2004 as compared with the third quarter of 2003. The increase during the third quarter of 2004 was due to continued investment in research and development programs aimed at introducing new products to our markets. As a percentage of sales, R&D expenses increased from 7.0% to 7.2%.

Restructuring and Other

During the third quarter of 2003, we received proceeds of $1.3 million and realized a gain of $0.8 million in connection with a sale of real estate.

Net Interest Expense

Net interest expense decreased $1.7 million in the third quarter of 2004 as compared with the third quarter of 2003. The lower net interest expense was principally a result of lower average debt outstanding. On March 4, 2004, we repaid our $75.0 million, 7.23% note with cash. Our net debt (total short and long term debt less cash and cash equivalents) as of October 2, 2004 was $49.4 million as compared to $176.9 million as of September 27, 2003. During the third quarter of 2004, the weighted average interest rate on our revolving credit agreement was approximately 2.6%.

Provision for Income Taxes

Our effective tax rate on net income for the third quarter of 2004 was 22.5%, the same as the third quarter of 2003. The effective annual tax rate for the full year of 2004 is also expected to be 22.5%.

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Nine Months Ended October 2, 2004 Compared to the Nine Months Ended September 27, 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 nine months ended October 2, 2004 as compared with the nine months ended September 27, 2003 is summarized in the table below.