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**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**Washington, DC 20549**

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**FORM 10-Q/A**

**Amendment No. 1**

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**(Mark One)**

**x**                              QUARTERLYREPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACTOF 1934

 

**For the quarterly period ended September 30, 2004**

**OR**

 

**o**                                 TRANSITIONREPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACTOF 1934

 

**For the transition periodfrom                     to                         .**

** **

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**Commission FileNumber  0-28494**

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**MILLENNIUM PHARMACEUTICALS, INC.**

(Exact name of registrant as specified in its charter)

 

| **Delaware**                       |   | **04-3177038**       |
|------------------------------------|--------|----------------------|
| (State or other  jurisdiction      |   | (I.R.S. Employer     |
| of incorporation  or organization) |   | Identification  No.) |

 

**40 Landsdowne Street, Cambridge,Massachusetts  02139** (Address of principal executive offices)(zip code)

**(617) 679-7000** (Registrant’s telephone number,including area code)

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Indicate by check mark whether the registrant (1) hasfiled all reports required to be filed by Section 13 or 15(d) of the SecuritiesExchange Act of 1934 during the preceding 12 months (or for such shorter periodthat the registrant was required to file such reports), and (2) has beensubject to such filing requirements for the past 90 days. Yes x  No o

Indicateby check mark whether the registrant is an accelerated filer (as defined inRule 12b-2 of the Exchange Act).Yes x  No o

Number ofshares of the registrant’s Common Stock, $0.001 par value, outstanding onNovember 4, 2004: 305,960,455

 

 

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**EXPLANATORYNOTE**

The Company is filing this Amendment No. 1 to our Quarterly Report onForm 10-Q for the fiscal quarter ended September 30, 2004, as originally filedon November 9, 2004, for the sole purpose of revising the Exhibit Index to addan Exhibit 10.5 and to file such exhibit. Also filed as exhibits with this 10-Q/A are new certifications inaccordance with Rule 13a-14(a) of the Exchange Act.

This Amendment No. 1 does not change the previously reported financialstatements or any of the other disclosure contained in the original Form 10-Q.

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**SIGNATURES**

Pursuantto the requirements of the Securities Exchange Act of 1934, the registrant hasduly caused this report to be signed on its behalf by the undersigned,thereunto duly authorized.
|                         |     | MILLENNIUM PHARMACEUTICALS, INC.                      |
|-------------------------|----------|-------------------------------------------------------|
|                    |     | (Registrant)                                          |
|                    |     |                                                  |
| Dated: November 9, 2006 |     | /s/ MARSHA H. FANUCCI                                 |
|                    |     | Marsha H. Fanucci                                     |
| * *                |     | *Senior Vice President and Chief Financial Officer*   |
| * *                | * * | *(principal financial and chief accounting  officer)* |

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**Exhibit Index**

**EXHIBITINDEX**
| Exhibit  No.     | ** ** | **Description**                                                                                                                                             |
|------------------|------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------|
|             |       |                                                                                                                                                        |
| 10.1*            |       | Agreement dated August 6, 2004 between the Company  and Marsha H. Fanucci                                                                                   |
|             |       |                                                                                                                                                        |
| 10.2*            |       | Agreement dated August 6, 2004 between the Company  and Kenneth M. Bate                                                                                     |
|             |       |                                                                                                                                                        |
| 10.3*            |       | Offer letter agreement dated September 28, 2004  between the Company and Laurie B. Keating                                                                  |
|             |       |                                                                                                                                                        |
| 10.4*            |       | Form of Director Stock Option Granted under 2000  Stock Incentive Plan                                                                                      |
|             |       |                                                                                                                                                        |
| 10.5   |       | Amendment No. 1 dated July 15, 2004 to the  Collaboration, Distribution and License Agreement by and between the Company  and Ortho Biotech Products, L. P. |
|             |       |                                                                                                                                                        |
| 31.1*            |       | Certification of principal executive officer  pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934,  as amended                      |
|             |       |                                                                                                                                                        |
| 31.2*            |       | Certification of principal financial officer  pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934,  as amended                      |
|             |       |                                                                                                                                                        |
| 31.3        |       | Certification of principal executive officer  pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934,  as amended                      |
|             |       |                                                                                                                                                        |
| 31.4        |       | Certification of principal financial officer  pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934,  as amended                      |
|             |       |                                                                                                                                                        |
| 32.1*            |       | Statement Pursuant to 18 U.S.C. §1350                                                                                                                  |
|             |       |                                                                                                                                                        |
| 32.2*            |       | Statement Pursuant to 18 U.S.C. §1350                                                                                                                  |

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*                    Exhibitfiled with original Form 10-Q filed with the SEC on November 9, 2004.

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