Exhibit
10.54  CONFIDENTIAL TREATMENT  THIRD AMENDMENT TO THE COMMERCIAL SERVICES AGREEMENT  This Third Amendment to the Commercial Services
Agreement (this Third Amendment) is made this 30th day of September, 2009 (the Amendment Effective Date), by and between
ASTRAZENECA PHARMACEUTICALS LP, a Delaware limited partnership (AstraZeneca), and CUBIST PHARMACEUTICALS, INC., a Delaware
corporation (Cubist).  WHEREAS, AstraZeneca and Cubist previously entered
into that certain Commercial Services Agreement between AstraZeneca and Cubist,
dated as of July 1, 2008 (as amended as of February 26, 2009 and May 20,
2009, the Agreement); and  WHEREAS, AstraZeneca and Cubist desire to amend
certain provisions of the Agreement relating to the Promotion Plan and Annual
Baseline Sales, as set forth herein.  NOW THEREFORE, in consideration of the premises and
the mutual covenants set forth herein and for other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged,
the parties hereby agree as follows:  1.Promotion Plan.The Agreement is hereby amended so that Section 3.1(b) is
deleted in its entirety and replaced with the following:  (b)         By October 16, 2009, for Calendar
Year 2010, and at least three (3) months prior to the commencement of each
Calendar Year thereafter, the parties shall update the Promotion Plan to
specify []* to be conducted by Cubist with respect to the Critical Care Target
Accounts and the Pediatric Target Accounts for such Calendar Year.  In addition to the foregoing annual updates,
the parties may modify the Promotion Plan from time to time by written
agreement.  2.Annual Baseline Sales.The Agreement is hereby amended so that Section 6.1(a) is
deleted in its entirety and replaced with the following:  (a)         Subject to modification pursuant to Section 6.1(b),
the Annual Baseline Sales for Calendar Year 2008 and 2009 and the baseline
Gross Sales for each Calendar Quarter (Quarterly
Baseline Sales) in each such Calendar Year are set forth in Exhibit A.  For each Calendar Year thereafter, the []*.  3.Definitions.All terms used, but not defined, in this Third Amendment shall have the
respective meanings set forth in the Agreement.  4.Construction.The principles set forth in Section 1.2 of the Agreement shall
apply to this Third Amendment.  
 *Confidential Treatment Requested. 
Omitted portions filed with the Securities and Exchange Commission (the
Commission).  1


5.Effective Date;
Incorporation of Terms; Continuing Effect.This Third
Amendment shall be deemed effective for all purposes as of the Amendment
Effective Date.  The amendment set forth
in this Third Amendment shall be deemed to be incorporated in, and made a part
of, the Agreement, and the Agreement and this Third Amendment shall be read,
taken and construed as one and the same agreement (including with respect to
the provisions set forth in Article XVI (Miscellaneous) of the Agreement
which shall, as applicable, be deemed to apply to this Third Amendment
(including with respect to the governing law)). 
Except as otherwise expressly amended by this Third Amendment, the
Agreement shall remain in full force and effect in accordance with its terms
and conditions.  6.Counterparts.This Third Amendment may be executed simultaneously in two or more
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.  [The remainder of this page has been
intentionally left blank.]  
 *Confidential Treatment Requested. 
Omitted portions filed with the Commission.  2


IN WITNESS WHEREOF, the parties, intending to be
bound, have caused this Third Amendment to be executed on their behalf by their
duly authorized agent as of the day and year first above written.  ASTRAZENECA
  PHARMACEUTICALS LP
  
  CUBIST PHARMACEUTICALS, INC.By:
  /s/
  Marion E. McCourt
  
  By:
  /s/
  David W. J. McGirrName:
  Marion
  E. McCourt
  
  Name:
  David
  W. J. McGirrTitle:
  VP,
  Cornerstone
  
  Title:
  SVP,
  CFO  
 *Confidential Treatment Requested. 
Omitted portions filed with the Commission.  3