<PAGE>


                                                                  Exhibit 10.10


          Confidential Materials omitted and filed separately with the
         Securities and Exchange Commission. Asterisk denote omissions.




                                          November 3, 2003


Schering-Plough Corporation
2000 Galloping Hill Road
Kenilworth, NJ  07033

         Re: Early ACS

Gentlemen:

         As you are aware, Schering Corporation ("Schering") and Millennium
Pharmaceuticals, Inc. ("Millennium") have agreed to undertake a Study (as
defined below) under the terms of the Collaboration Agreement, dated April 10,
1995, as amended (the "Agreement") by and among Millennium, Schering and
Schering's affiliate, Schering-Plough Ltd.

         This letter confirms that Schering and Millennium have agreed to [**]
the cost of the Early ACS clinical study for INTEGRILIN that has been agreed
upon by the Joint Strategic Committee ("JSC"), after accounting for funds
contributed to this study by any other entities, and the parties hereby
authorize initiation of activities in connection with the study as of October 1,
2003. A draft budget for the Early ACS study (the "Study") is attached hereto
(as Exhibit A) and, for the term of the Study, is deemed to be part of the JSC
approved Development Plan. The JSC is hereby authorized to approve in writing
any changes to the budget and to approve the final protocol.


<PAGE>


                                                              November 3, 2003


                                      -2-


It is acknowledged and agreed that the Study will be conducted under the terms
of the Agreement; provided that notwithstanding the provisions of Sections
3.5(a) of the Agreement, as well as any other terms or conditions of the
Agreement to the contrary, the parties' financial obligations with respect to
the cost of the Study shall be governed by the terms of this letter agreement.
Except as expressly modified by the terms of this letter agreement, all of the
terms and conditions of the Agreement shall remain in full force and effect.
This agreement is effective as of October 1, 2003.


Millennium Pharmaceuticals, Inc.                  Schering Corporation


By: /s/ A. J. HILLER                              By: /s/ DAVID POORVIN
    ----------------                                  -----------------

Name: A. J. HILLER                                Name: DAVID POORVIN
      ------------                                      -------------

Title: SVP, GLOBAL STRATEGIC MKTG.                Title: VICE PRESIDENT
       --------------------------                        --------------

Date: 11/3/03                                     Date: 17 NOVEMBER 2003
      -------                                           ----------------





                                                  Schering-Plough Ltd.


                                                  By: /s/ KARL MEIER
                                                      --------------

                                                  Name: KARL MEIER
                                                        ----------

                                                  Title: DIRECTOR
                                                         --------

                                                   Date: 11/21/03
                                                         --------


<PAGE>


                                    EXHIBIT A
                                  Draft Budget


ESTIMATED BUDGET FOR EARLY ACS TRIAL

<TABLE>
<CAPTION>
----------------------------------------------------------------------------------------------------------------------
[**]                                                                          Estimate (million)
----------------------------------------------------------------------------------------------------------------------
<S>                                                                        <C>
[**]                                                                          $   [**]
----------------------------------------------------------------------------------------------------------------------
[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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[**]                                                                          $   [**]
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TOTAL                                                                         $   [**]
----------------------------------------------------------------------------------------------------------------------
</TABLE>


Notes: The parties agree that undisputed invoices submitted under this cost
sharing agreement will be paid within thirty (30) days. Payments for disputed
items may be withheld for up to ten (10) business days while the parties work
diligently and in good faith to resolve the dispute. For the purpose of
determining cost sharing of internal FTE costs arising from the Study, the
parties agree that the fully-loaded, annualized FTE rate is $[**].