**UNITEDSTATESSECURITIES AND EXCHANGE COMMISSION**

**Washington, D.C.20549**

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**FORM 10-K/A**

**Amendment No. 1**

**(MarkOne)**
| x                                                                                                                                                                                                                                                                                                                               | **ANNUAL REPORT PURSUANT TO SECTION 13 OR  15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**     |
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                                                                                                                                            | ** **                                                                                              |
| **For the  fiscal year ended: December 31, 2005**                                                                                                                                                                                                                                                                          |
| ** **                                                                                                                                                                                                                                                                                                                      | ** **                                                                                              |
| **or**                                                                                                                                                                                                                                                                                                                          |
|                                                                                                                                                                                                                                                                                                                            | ** **                                                                                              |
| o                                                                                                                                                                                                                                                                                                                               | **TRANSITION REPORT PURSUANT TO SECTION 13 OR  15(d) OF THE SECURITIES EXCHANGE ACT OF 1934** |
|                                                                                                                                                                                                                                                                                                                            |                                                                                                    |
| **For the  transition period from                           to                         ** |

 

**Commission file number: 0-28494**

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**MILLENNIUMPHARMACEUTICALS, INC.**

(Exact name of registrant asspecified in its charter)

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

 

**40Landsdowne Street, Cambridge, Massachusetts 02139**

(Address of principalexecutive offices) (zip code)

Registrant’s telephonenumber, including area code:  **(617) 679-7000**

Securities registeredpursuant to Section 12(b) of the Act: **None**

Securities registeredpursuant to Section 12(g) of the Act:

**CommonStock, $.001 par value**

(Title of class)

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Indicate by check mark if the registrant is awell-known seasoned issuer, as defined in Rule 405 of the SecuritiesAct.  Yes x  No o

Indicate by check mark if the registrant is notrequired to file reports pursuant to Section 13 orSection 15(d) of the Act.  Yes o  No x

Indicate by check mark whether the registrant(1) has filed all reports required to be filed by Section 13 or15(d) of the Securities Exchange Act of 1934 during the preceding12 months (or for such shorter period that the registrant was required tofile such reports), and (2) has been subject to such filing requirementsfor the past 90 days.  Yes x  No o

Indicate by check mark if disclosure of delinquentfilers pursuant to Item 405 of Regulation S-K is not contained herein, andwill not be contained, to the best of registrant’s knowledge, in definitiveproxy or information statements incorporated by reference in Part III ofthis Form 10-K or any amendment to this Form 10-K.  o

Indicate by check mark whether the registrant is alarge accelerated filer, an accelerated filer, or a non-accelerated filer. Seedefinition of “accelerated filer and large accelerated filer” in Rule 12b-2of the Exchange Act. (Check one):

Large accelerated filer  x          Acceleratedfiler  o          Non-acceleratedfiler  o

Indicate by check mark whether the registrant is ashell company (as defined in Rule 12b-2 of the Act).  o Yes  x No

The aggregate market value of voting Common Stockheld by non-affiliates of the registrant as of June 30, 2005 was$2,813,245,778 based on the last reported sale price of the Common Stock on theNasdaq Stock Market on that date.

Number of shares outstanding of the registrant’sclass of Common Stock as of March 3, 2006: 312,129,971.

**Documents incorporated by reference:**

Portions of the information required by Part IIIof Form 10-K will appear in the registrant’s definitive ProxyStatement on Schedule 14A for the 2006 Annual Meeting of Stockholders andare hereby incorporated by reference into this report.

 

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**EXPLANATORYNOTE**

The Company is filing this Amendment No. 1 to our Annual Report on Form10-K for the fiscal year ended December 31, 2005, as originally filed with theSEC on March 8, 2006, for the sole purpose of revising the Exhibit Index to addan Exhibit 10.22(b) and designate the originally filed Exhibit 10.22 as Exhibit10.22(a).  Filed as exhibits with this10-K/A are new certifications in accordance with Rule 13a-14(a) of the ExchangeAct.

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

2

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**SIGNATURES**

Pursuantto the requirements of Section 13 or 15(d) of the Securities ExchangeAct of 1934, the registrant has duly caused this report to be signed on itsbehalf by the undersigned, thereunto duly authorized.
| Date: November 9, 2006 | MILLENNIUM PHARMACEUTICALS, INC. |
|-----------------------------|---------------------------------------|
|                        |                                  |   |
|                        | By:                                   | /s/ MARSHA H. FANUCCI |   |
|                        |                                  | Marsha H. Fanucci |
|                        |                                  | *Senior Vice President and  Chief Financial Officer* |

 

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**EXHIBIT INDEX**

|                      | ** ** | ** **                                                                                                                                                                                                                                                            | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**                    |
|----------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|------------------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                                                                                                                                       | ** ** | **Form**                      | ** ** | **SEC  filing date**          | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
| ** **           | ** ** | ***Articles of Incorporation and  By-laws***                                                                                                                                                                                                                          | ** ** | ** **                    | ** ** | ** **                         | ** ** | ** ** | ** ** | ** ** |
| ** **           | ** ** | *** ***                                                                                                                                                                                                                                                          | ** ** | ** **                    | ** ** | ** **                         | ** ** | ** ** | ** ** | ** ** |
| 3.1                  |       | Amended and Restated Certificate of Incorporation of  the Company, as amended                                                                                                                                                                                         |       | 10-Q  8-K  10-Q               |       | 06/20/1996  04/13/2000  04/19/2001 |   | 4.1  3  3.1 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
| 3.2                  |       | Amended and Restated Bylaws of the Company, as  amended                                                                                                                                                                                                               |       | 10-Q  10-Q  10-Q              |       | 06/20/1996  05/02/2000  11/09/2000 |   | 4.2  3.1  3.1 | ** ** | ** ** |
| ** **           | ** ** | ** **                                                                                                                                                                                                                                                            | ** ** | ** **                    | ** ** | ** **                         | ** ** | ** ** | ** ** | ** ** |
| ** **           | ** ** | ***Instruments defining the rights  of security holders, including indentures***                                                                                                                                                                                      | ** ** | ** **                    | ** ** | ** **                         | ** ** | ** ** | ** ** | ** ** |
| ** **           | ** ** | *** ***                                                                                                                                                                                                                                                          | ** ** | ** **                    | ** ** | ** **                         | ** ** | ** ** | ** ** | ** ** |
| 4.1                  |       | Specimen Certificate for shares of Common Stock,  $.001 par value, of the Company                                                                                                                                                                                     |       | S-1/A(333-02490)              |       | 05/02/1996                         |   | 4.1 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
| 4.2                  |       | Indenture, dated as of January 20, 2000,  between the Company and State Street Bank and Trust Company, as Trustee  relating to the 5.50% Convertible Subordinated Notes due January 15,  2007 (including the form of debenture)                             |       | 10-K                          |       | 02/25/2000                         |   | 4.2 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
| 4.3                  |       | Rights Agreement dated April 5, 2001 by and  between the Company and State Street Bank and Trust Company, N.A.                                                                                                                                                   |       | 8-K                           |       | 04/05/2001                         |   | 4.1 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
| 4.4                  |       | (a) Indenture,  dated February 24, 2000, between the Company (as successor to COR Therapeutics, Inc.)  and U.S. Bank, N.A. (formerly known as Firstar Bank, N.A.), as Trustee,  relating to the 5.00% Convertible Subordinated Notes due March 1, 2007 |       | (a)10-Q*                      |       | 05/10/2000                         |   | 4.1 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
|                 |       | (b) First  Supplemental Indenture, dated as of February 12, 2002                                                                                                                                                                                                 |       | (b)8-K                        |       | 02/13/2002                         |   | 4.5 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
|                 |       | (c) Second  Supplemental Indenture, dated as of February 12, 2002                                                                                                                                                                                                |       | (c)8-K                        |       | 02/13/2002                         |   | 4.6 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
|                 |       | (d) Third  Supplemental Indenture, dated as of April 22, 2002                                                                                                                                                                                                    |       | (d)8-K                        |       | 04/23/2002                         |   | 4.2 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                                                                                                  |       |                          |       |                               |   |   | ** ** | ** ** |
| 4.5                  |       | (a) Indenture,  dated June 11, 2001, between the Company (as successor to COR Therapeutics, Inc.)  and U.S. Bank,                                                                                                                                           |       | (a)10-Q*                      |       | 08/03/2001                         |   | 4.1 | ** ** | ** ** |

 

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|                      | ** ** | ** **                                                                                                                                                                            | ** ** | **Incorporated by Reference**    | ** ** | **Filed  with**                                |
|----------------------|------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|----------------------------------|------------|------------------------------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                                                       | ** ** | **Form**                         | ** ** | **SEC  filing date**                      | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
|                 |       | N.A. (as successor to  Firstar Bank, N.A.), as Trustee, relating to the 4.50% Convertible Senior  Notes due June 15, 2006                                                        |       |                             |       |                                           |   |   | ** ** | ** ** |
|                 |       | (b) First  Supplemental Indenture, dated as of February 12, 2002                                                                                                                 |       | (b)S-3(333-82654)                |       | 02/13/2002                                     |   | 4.2 | ** ** | ** ** |
|                 |       | (c) Second  Supplemental Indenture, dated as of February 12, 2002                                                                                                                |       | (c)S-3(333-82654)                |       | 02/13/2002                                     |   | 4.3 | ** ** | ** ** |
|                 |       | (d) Third  Supplemental Indenture, dated as of April 22, 2002                                                                                                                    |       | (d)8-K                           |       | 04/23/2002                                     |   | 4.1 | ** ** | ** ** |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   | ** ** | ** ** |
|                 |       | ***Material  contracts—financing agreements***                                                                                                                                   |       |                             |       |                                           |   |   | ** ** | ** ** |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   | ** ** | ** ** |
| 10.1                 |       | Form of Master Equipment Lease Financing  Agreement, dated September 19, 1996 by and between the Company and GE  Capital Corporation, as amended                       |       | 10-Q  10-Q  10-K  10-K           |       | 11/13/1996  08/14/1997  02/25/2000  03/15/2001 |   | 10.2  10.9  10.3, 10.4  10.2 |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.2                 |       | Lease Agreement dated August 26, 1993, as  amended, by and between the Company and the Massachusetts Institute of  Technology, as amended, for 640 Memorial Drive, Cambridge, MA |       | S-1 (333-2490)  10-K  10-K  10-K |       | 3/18/1996  3/24/1999  2/25/2000  3/15/2001     |   | 10.32  10.57  10.6  10.4 |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.3                 |       | Lease Agreement dated August 4, 2000 by and  between the Company and Forest City Enterprises, Inc. for  35 Landsdowne Street, Cambridge, MA                            |       | 10-Q                             |       | 11/9/2000                                      |   | 10.3 |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.4                 |       | Lease Agreement dated August 4, 2000 by and  between the Company and Forest City Enterprises, Inc. for  40 Landsdowne Street, Cambridge, MA                            |       | 10-Q                             |       | 11/9/2000                                      |   | 10.4 |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.5                 |       | First Amendment to Lease FC 40 Landsdowne, Inc.  to the Company dated November 5, 2001                                                                                 |       |                             |       |                                           |   |   |   | X(1) |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.6                 |       | Agreement for Lease dated February 9, 2001  among Granta Park Limited, MEPC Limited, Millennium Pharmaceuticals Limited  and the Company (including the form of lease)           |       | 10-K                             |       | 3/15/2001                                      |   | 10.8 |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
|                 |       | ***Material contracts—research and  development/collaboration agreements***                                                                                                      |       |                             |       |                                           |   |   |   |   |
|                 |       |                                                                                                                                                                                  |       |                             |       |                                           |   |   |   |   |
| 10.7                 |       | (a)  Collaboration and License                                                                                                                                                        |       | (a)10-Q                          |       | 07/26/2000                                     |   | 10.1 |   |   |

 

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|                      | ** ** | ** **                                                                                                                                                                             | ** ** | **Incorporated by Reference**     | ** ** | **Filed  with**                                            |
|----------------------|------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|-----------------------------------|------------|------------------------------------------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                                                        | ** ** | **Form**                          | ** ** | **SEC  filing date**                                  | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
|                 |       | Agreement dated  June 22, 2000 by and between the Company and the sanofi-aventis Group  (as successor to Aventis Pharmaceuticals, Inc.), as amended†                    |       |      10-Q     |       | 10/25/2001                                                 |   | 10.3 |   |   |
|                 |       | (b) Second  Amendment effective as of December 22, 2002 dated April 22, 2003 to  the Collaboration and License Agreement†                                               |       | (b)10-Q                           |       | 08/12/2003                                                 |   | 10.1 |   |   |
|                 |       | (c) Technology  Development Agreement dated June 22, 2000†                                                                                                                   |       | (c)10-Q                           |       | 07/26/2000                                                 |   | 10.2 |   |   |
|                 |       | (d) Registration  Rights Agreement dated June 22, 2000                                                                                                                            |       | (d)10-Q                           |       | 07/26/2000                                                 |   | 10.4 |   |   |
|                 |       | (e) Letter  Agreement dated May 27, 2004 relating to the Collaboration and License  Agreement†                                                                               |       | (e)10-Q                           |       | 08/04/2004                                                 |   | 10.1 |   |   |
|                 |       | (f) Letter Agreement dated July 21, 2005†                                                                                                                                    |       | (f)10-Q                           |       | 08/08/2005                                                 |   | 10.7 |   |   |
|                 |       | (g) Third  Amendment effective as of October 31, 2005 and dated November 7,  2005 to the Collaboration and License Agreement †                                          |       |                              |       |                                                       |   |   |   | X(1) |
|                 |       |                                                                                                                                                                                   |       |                              |       |                                                       |   |   |   |   |
|                 |       | ***Material contracts—INTEGRILIN® (eptifibatide) Injection***                                                                                                           |       |                              |       |                                                       |   |   |   |   |
|                 |       |                                                                                                                                                                                   |       |                              |       |                                                       |   |   |   |   |
| 10.8                 |       | License and Supply Agreement between the Company (as  successor to COR Therapeutics, Inc.) and Solvay, Société Anonyme, dated  July 27, 1994, as amended†     |       | 10-Q*                             |       | 11/13/1998                                                 |   | 10.24  10.25  10.26  10.27  10.28  10.29 |   |   |
|                 |       |                                                                                                                                                                                   |       |                              |       |                                                       |   |   |   |   |
| 10.9                 |       | New Long Term Supply Agreement between the Company  and Solvay, Société Anonyme, dated January 1, 2003†                                                            |       | 10-K                              |       | 03/07/2003                                                 |   | 10.9 |   |   |
|                 |       |                                                                                                                                                                                   |       |                              |       |                                                       |   |   |   |   |
| 10.10                |       | Collaboration Agreement between Schering-Plough  Ltd., Schering Corporation and the Company (as successor to COR Therapeutics, Inc.)  dated April 10, 1995, as amended† |       | 10-Q*  10-K*  10-K*  10-Q*  10-Q* |       | 08/08/1995  03/25/1999  03/30/2000  08/10/2000  11/08/2000 |   | 10.41  10.33  10.35  10.1  10.1, 10.2 |   |   |
|                 |       |                                                                                                                                                                                   |       |                              |       |                                                       |   |   |   |   |
| 10.11                |       | Letter agreement dated June 4, 2002 relating to  the Collaboration Agreement dated April 10, 1995 between Schering  Corporation and the Company†                        |       | 10-K                              |       | 03/10/2004                                                 |   | 10.8 |   |   |

 

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|                      | ** ** | ** **                                                                                                                                                                                               | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**           |
|----------------------|------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|---------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                                                                          | ** ** | **Form**                      | ** ** | **SEC  filing date** | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
| 10.12                |       | Addendum to Collaboration Agreement among the  Company, Schering Corporation and Schering-Plough, Ltd. dated  June 1, 2003†                                                                    |       | 10-K                          |       | 03/10/2004                |   | 10.9 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.13                |       | Letter agreement dated November 3, 2003  relating to the Collaboration Agreement dated April 10, 1995 between  Schering Corporation and the Company†                                      |       | 10-K                          |       | 03/10/2004                |   | 10.10 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.14                |       | Agreement about  European Commercialization of Integrilin by and among the Company, Schering  Corporation and Schering-Plough, Ltd. dated June 21, 2004†                                       |       | 10-Q                          |       | 08/04/2004                |   | 10.2 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.15                |       | Letter agreement dated September 17, 2004  relating to the Addendum dated June 1, 2003 to the Collaboration  Agreement among the Company, Schering Corporation and Schering-Plough,  Ltd† |       | 10-K                          |       | 03/08/2005                |   | 10.10 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.16                |       | Letter agreement dated November 30, 2004  relating to the Addendum dated June 1, 2003 to the Collaboration  Agreement among the Company, Schering Corporation and Schering-Plough,  Ltd†  |       | 10-K                          |       | 03/08/2005                |   | 10.11 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.17                |       | Amended and Restated Integrilin Agreement dated  July 22, 2005 among the Company, Schering Corporation and  Schering-Plough, Ltd.†                                                             |       | 10-Q                          |       | 11/08/2005                |   | 10.1 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.18                |       | Side Agreement dated October 13, 2005 among the  Company, Schering Corporation and Schering-Plough Ltd.†                                                                                       |       | 10-Q                          |       | 11/08/2005                |   | 10.2 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.19                |       | Supply Agreement dated September 1, 2005 by and  between the Company and Schering Corporation†                                                                                                 |       | 10-Q                          |       | 11/08/2005                |   | 10.3 |   |   |
|                 |       |                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
| 10.20                |       | (a) License,  Development and Commercialization Agreement by and between GlaxoSmithKline  plc and the Company dated June 22, 2004†                                                             |       | 10-Q                          |       | 08/04/2004                |   | 10.3 |   |   |

 

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|                      | ** ** | ** **                                                                                                                                                                                                                                                                                                       | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**           |
|----------------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|---------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                                                                                                                                                                                  | ** ** | **Form**                      | ** ** | **SEC  filing date** | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
|                 |       | (b) Letter  agreement dated March 4, 2005 relating to the License, Development and  Commercialization Agreement by and between GlaxoSmithKline plc and the  Company dated June 22, 2004†                                                                                                          |       | 10-K                          |       | 03/08/2005                |   | 10.12(b) |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
|                 |       | ***Material contracts—VELCADE® (bortezomib) for Injection***                                                                                                                                                                                                                                      |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.21                |       | Patent License Agreement between the Public Health  Service and the Company dated December 2, 2002†                                                                                                                                                                                                    |       | 10-K                          |       | 03/10/2004                |   | 10.11 |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.22                |       | (a)  Collaboration, Distribution and License Agreement by and between the Company  and Ortho Biotech Products, L.P. dated June 30, 2003†                                                                                                                                                               |       | 10-Q

                   |       | 08/12/2003

         |   | 10.2

  |   |   |
|                 |       | (b) Amendment  dated July 15, 2004 to Collaboration, Distribution and License Agreement by  and between the Company and Ortho Biotech Products, L.P. dated June 30,  2003                                                                                                                                   |       | 10-Q/A                        |       | 11/09/2006                |   | 10.5 |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
|                 |       | ***Material  contracts—miscellaneous***                                                                                                                                                                                                                                                                     |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.23                |       | Registration Rights Agreement among the Company (as  successor to COR Therapeutics, Inc.) and Goldman, Sachs & Co.,  Chase H&Q, a division of Chase Securities Inc., CIBC World Markets Corp.,  FleetBoston Robertson Stephens Inc. and Warburg Dillon Read LLC, dated  February 24, 2000 |       | 10-Q*                         |       | 05/10/2000                |   | 10.2 |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.24                |       | Registration Rights Agreement among the Company (as  successor to COR Therapeutics, Inc.) and Goldman, Sachs & Co.,  Robertson Stephens, Inc., Credit Suisse First Boston Corporation, CIBC  World Markets Corp., and Needham & Company, Inc., dated  June 11, 2001        |       | 10-Q*                         |       | 08/03/2001                |   | 10.2 |   |   |
|                 |       |                                                                                                                                                                                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.25                |       | Registration Rights Agreement dated January 20,  2000 between the Company and Goldman, Sachs & Co.,                                                                                                                                                                                                |       | 10-K                          |       | 02/25/2000                |   | 10.29 |   |   |

 

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|                      | ** ** | ** **                                                                                                                            | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**           |
|----------------------|------------|---------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|---------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                       | ** ** | **Form**                      | ** ** | **SEC  filing date** | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
|                 |       | ING Barings LLC, FleetBoston Robertson Stephens  Inc., and Credit Suisse First Boston Corporation                                     |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
|                 |       | ***Material contracts—management  contracts and compensatory plans***                                                            |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.26                |       | Key Employee Change in Control Severance Plan#                                                                                        |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.27                |       | Non-Qualified Deferred  Compensation Plan#                                                                                            |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.28                |       | Form of Restricted Stock Agreement#                                                                                              |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.29                |       | Description of Non-Employee Director  Compensation#                                                                                   |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.30                |       | Description of Success Sharing Bonus Program of  Millennium Pharmaceuticals, Inc.#                                               |       | 8-K                           |       | 02/06/2006                |   | 10.1 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.31                |       | 2003 Employee Stock Purchase Plan for Non-U.S.  Subsidiaries and Affiliated Entities, as amended#                                     |       | 10-Q                          |       | 11/08/2005                |   | 10.5 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.32                |       | 2000 Stock Incentive Plan, as amended#                                                                                                |       | 10-K                          |       | 03/07/2003                |   | 10.14 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.33                |       | Form of Terms of Stock Option Granted Under  2000 Stock Incentive Plan#                                                          |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.34                |       | 1997 Equity Incentive Plan, as amended#                                                                                               |       | 10-K                          |       | 03/07/2003                |   | 10.15 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.35                |       | 1996 Equity Incentive Plan, as amended#                                                                                               |       | 10-K                          |       | 03/07/2003                |   | 10.16 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.36                |       | 1996 Director Option Plan#                                                                                                            |       | S-1/A(333-02490)              |       | 04/09/1996                |   | 10.1 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.37                |       | 1996 Employee Stock Purchase Plan, as amended#                                                                                        |       | 10-Q                          |       | 11/08/2005                |   | 10.4 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.38                |       | 1993 Incentive Stock Plan, as amended#                                                                                                |       | 10-K                          |       | 03/07/2003                |   | 10.20 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.39                |       | 1991 Equity Incentive Plan, as amended, assumed by  the Company as successor to COR Therapeutics, Inc.#                          |       | 10-Q*                         |       | 05/09/2001                |   | 10.2 |   |   |
|                 |       |                                                                                                                                  |       |                          |       |                      |   |   |   |   |
| 10.40                |       | 1994 Non-employee Directors’ Stock Option Plan, as  amended, assumed by the Company as successor to COR Therapeutics, Inc.# |       | 10-Q*                         |       | 05/09/2001                |   | 10.4 |   |   |

 

9

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|                      | ** ** | ** **                                                                                                                                        | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**           |
|----------------------|------------|---------------------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|---------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                   | ** ** | **Form**                      | ** ** | **SEC  filing date** | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
| 10.41                |       | 1997 Equity Incentive Plan, as amended, assumed by  the Company as successor to Millennium BioTherapeutics, Inc.#                            |       | 10-K                          |       | 03/07/2003                |   | 10.23 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.42                |       | 1997 Equity Incentive Plan, as amended, assumed by  the Company as successor to Millennium Predictive Medicine, Inc.#                        |       | 10-K                          |       | 03/07/2003                |   | 10.24 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.43                |       | Form of Employment Offer Letter entered into  with certain executive officers of the Company, together with a schedule of  parties thereto # |       | 10-K                          |       | 03/08/2005                |   | 10.35 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.44                |       | Form of Indemnification Agreement between the  Company (as successor to COR Therapeutics, Inc.) and Charles J. Homcy#                   |       | S-1 (33-40627)*               |       | 05/16/1991                |   | 10.1 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.45                |       | Agreement dated August 6, 2004 between the  Company and Marsha H. Fanucci#                                                                   |       | 10-Q                          |       | 11/09/2004                |   | 10.1 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.46                |       | Offer letter agreement dated September 28, 2004  between the Company and Laurie B. Keating#                                                  |       | 10-Q                          |       | 11/09/2004                |   | 10.3 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.47                |       | Offer Letter Agreement dated June 23, 2005  between the Company and Deborah Dunsire#                                                         |       | 10-Q                          |       | 08/08/2005                |   | 10.1 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.48                |       | Restricted Stock Agreement dated July 18, 2005  between the Company and Deborah Dunsire#                                                     |       | 10-Q                          |       | 08/08/2005                |   | 10.2 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.49                |       | Restricted Stock Agreement dated July 18, 2005  between the Company and Deborah Dunsire#                                                     |       | 10-Q                          |       | 08/08/2005                |   | 10.3 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.50                |       | Incentive Stock Option Granted under 2000 Stock  Incentive Plan to Deborah Dunsire on July 18, 2005#                                         |       | 10-Q                          |       | 08/08/2005                |   | 10.4 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.51                |       | Nonstatutory Stock Option Granted under 2000 Stock  Incentive Plan to Deborah Dunsire on July 18, 2005#                                      |       | 10-Q                          |       | 08/08/2005                |   | 10.5 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.52                |       | Description of Deferred Compensation Plan for  Deborah Dunsire #                                                                                  |       | 10-Q                          |       | 08/08/2005                |   | 10.6 |   |   |
|                 |       |                                                                                                                                              |       |                          |       |                      |   |   |   |   |
| 10.53                |       | Offer letter agreement dated                                                                                                                      |       |                          |       |                      |   |   |   | X(1) |

 

10

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|                      | ** ** | ** **                                                                                                                                       | ** ** | **Incorporated by Reference** | ** ** | **Filed  with**           |
|----------------------|------------|--------------------------------------------------------------------------------------------------------------------------------------------------|------------|-------------------------------|------------|---------------------------|
| **Exhibit No.** | ** ** | **Description**                                                                                                                                  | ** ** | **Form**                      | ** ** | **SEC  filing date** | ** ** | **Exhibit  number** | ** ** | **this  10-K** |
|                 |       | January 23, 2006 between the Company and  Christophe Bianchi#                                                                               |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 10.54                |       | Offer letter agreement dated February 6, 2006  between the Company and Stephen M. Gansler#                                                  |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
|                 |       | ***Additional Exhibits***                                                                                                                        |       |                          |       |                      |   |   |   |   |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 21                   |       | Subsidiaries of the Company                                                                                                                      |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 23.1                 |       | Consent of Ernst & Young LLP, Independent  Registered Public Accounting Firm                                                            |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 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 |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 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 |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 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 |       |                          |       |                      |   |   |   | X(2) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 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 |       |                          |       |                      |   |   |   | X(2) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 32.1                 |       | Statement Pursuant to 18 U.S.C. §1350                                                                                                       |       |                          |       |                      |   |   |   | X(1) |
|                 |       |                                                                                                                                             |       |                          |       |                      |   |   |   |   |
| 32.2                 |       | Statement Pursuant to 18 U.S.C. §1350                                                                                                       |       |                          |       |                      |   |   |   | X(1) |

 

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#                    Managementcontract or compensatory plan or arrangement filed as an exhibit to this reportpursuant to Items 15(a) and 15(c) of Form 10-K

11

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†                     Confidentialtreatment requested as to certain portions, which portions have been separatelyfiled with the Securities and Exchange Commission

*                    CORTherapeutics, Inc. filing (Commission file no. 0-19290)

(1)    Exhibitfiled with Form 10-K originally filed with the SEC on March 8, 2006.

(2)    Exhibit filed with this Form 10-K/A.

12

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