Exhibit
10.3


CONFIDENTIAL
TREATMENT


AMENDMENT NO. 2


Cardinal Health
PTS, LLC (“Cardinal Health”) and Cubist Pharmaceuticals, Inc., (“Cubist”) are
parties to a Processing Services Agreement dated August 11, 2004, as amended by
Amendment No. 1 dated May 23, 2005 (the “Agreement”).


The parties now
desire to amend the Agreement pursuant to the terms of this Amendment No. 2 to
set forth the terms and conditions upon which Cardinal Health would move the
manufacture of the Product primarily to a second facility.


Cardinal Health and Cubist have executed a December 1, 2006 Quotation
QTE-2006-0361.00 (“Tech Transfer Feasibility Quote”) pursuant to which Cardinal
Health will produce a Process Transfer Feasibility Report and a Plant
Certification Document pursuant to the terms of the Tech Transfer Feasibility
Quote.  Cubist will pay Cardinal Health
[]* for the work performed under the Tech Transfer Feasibility Quote.  The Process Transfer Feasibility Report and
the Plant Certification Document will detail how Cardinal Health’s second
facility will be validated and the costs and responsibilities of each of the
Parties associated with such validation.


Now therefore, in consideration of the mutual conditions and covenants
set forth herein, Cardinal Health and Cubist agree as follows:


1.                     Cardinal Health shall perform the activities
described in the Plant Certification Document (“Certification Activities”) in
accordance with the terms and the schedules contained in the Plant
Certification Document.


2.                     Provided that Cardinal Health performs the
Certification Activities in accordance with the Plant Certification Document,
Cubist shall use diligent and commercially reasonable efforts to achieve the
approval of the Cardinal Health facility located at 8900 Capital Blvd, Raleigh,
NC for the Processing of the commercial supplies of the Product (“FDA Approval”)
as soon as reasonably possible.


3.                     Effective upon FDA Approval,


a.               Section 1.20 of the Agreement shall be
amended by adding “(“NM Facility”) and at 8900 Capital Blvd, Raleigh, NC (“NC
Facility”) immediately after “Albuquerque, New Mexico.”


b.              The Agreement shall be amended by adding the
following sentence to the end of Section 2.1:






*Confidential Treatment Requested. 
Omitted portions filed with the Securities and Exchange Commission (the
“Commission”).



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Upon approval of the NC Facility, Cardinal
Health shall Process Product in a quantity not more than []* batches []*, and
not more than []* batch []* during the Term at the NM Facility without Cubist’s
prior written consent.


c.               The Agreement shall be amended by adding the
following sentence to the end of Section 3.3:


All Product Processed (other than packaging)
at the NC Facility shall be packaged by Cardinal Health at its packaging
facility located at 3001 Red Lion Road, Philadelphia, PA.


d.              The first sentence of Section 15.1 of the
Agreement shall be deleted in its entirety and replaced with the following:


This Agreement shall commence on the
Effective Date and shall continue until August 11, 2010, unless earlier
terminated under Section 15.2 below (the “Term”).


e.               A new Section 4.8 shall be added to the
Agreement, as follows:


4.8             Minimum Requirement. Upon regulatory approval of
the NC Facility, Cubist shall order a minimum of []* of Product to be Processed
(“Minimum Requirement”) during []* commencing on []* and Cardinal Health shall
accept Cubist’s Purchase Orders including such minimum number of units and
shall Process and Deliver at least such minimum number of units according to
such Purchase Orders. Notwithstanding the foregoing, Cardinal Health may
propose alternative delivery date(s) that are within []* of what is requested
in Cubist’s Purchase Order in order to permit Cardinal Health to manage its
available manufacturing capacity in respect of commitments previously made to
its clients; in such cases, the parties shall reasonably agree to the revised
delivery date(s).    The Minimum
Requirement shall be pro-rated in any partial []*. If Cubist does not order
such Minimum Requirement during []*, within []* after the end of []*, Cubist
shall pay Cardinal Health the difference between []*.  Notwithstanding anything herein to the
contrary, if at any time during the initial term but following the first []*
batches of Product produced under this Agreement, if Cubist appropriately rejects
Product due to Cardinal Health’s breach of its obligations hereunder to provide
Product conforming to the Specifications and Applicable Laws []* or more times
in []*, Cubist shall have the right, at Cubist’s sole discretion, to withdraw
any or all Purchase Orders which have been submitted at the time of []*, and
any remaining Minimum Requirement during the Term shall no longer apply.


f.                 The Agreement shall be amended by inserting
the following sentence after the first sentence of Section 7.1:


Cubist shall pay []* for the
[]* of Product purchased from Cardinal Health under this Agreement []*.






*Confidential Treatment Requested. 
Omitted portions filed with the Commission.



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4.                       Termination Prior to FDA Approval.


a.               If FDA Approval does not occur by []*, the
provisions set forth in Sections 2, 3 and 7 of this Amendment No. 2 shall have
no further force or effect unless otherwise agreed to by the parties in
writing.


b.              If Cubist elects to cease efforts to transfer
the Product to the NC Facility or otherwise fails to support or elects to
abandon its pursuit of FDA Approval for any reason other than a Cardinal
Reason, as defined below, then []*.


c.               If a Cardinal Reason occurs, then []*.


d.              .As used in this Amendment No. 2, a “Cardinal
Reason” shall mean: (i) Cardinal Health’s failure to completely perform the
Certification Activities in accordance with the Plant Certification Document;
(ii) Cardinal Health’s election to abandon its pursuit of FDA Approval for any
reason; or (iii) the NC Facility’s failure to comply with FDA requirements or
Cardinal Health’s failure to satisfactorily address any FDA documented
observations at the NC Facility.


5.                     The first sentence of Section 7.2 of the
Agreement is hereby amended to delete the phrase “, effective on the
anniversary date of this Agreement” in its entirety and to replace such
language with “commencing on January 1, 2008”.


6.                     Section 16.1 of the Agreement is hereby
amended by adding []* within the parenthetical, immediately before []*


7.                     []*, Exhibit B-1 of the Agreement shall be
deleted in its entirety and replaced with Exhibit B-1 attached to this
Amendment No. 2.


Any
conflict between the provisions of this Amendment No. 2 and the Agreement shall
be resolved in favor of this Amendment No. 2 and capitalized terms used in this
Amendment No. 2 shall have the same meaning given to them in the Agreement,
unless otherwise defined in this Amendment No. 2.


This Amendment No.
2 shall be effective April 18, 2007 (“Amendment No. 2 Effective Date”).  Unless otherwise expressly set forth herein,
all other terms and conditions set forth in the Agreement shall remain in full
force and effect.  Following the
Amendment No. 2 Effective Date, the term “Agreement” shall be deemed a
reference to the Agreement as amended by this Amendment No. 2.


This Amendment No. 2 may
be signed in counterparts, each of which shall be deemed to be an original and
all of which together shall constitute but one and the same instrument, and
such counterparts may be exchanged by facsimile.


In witness whereof, this Amendment No. 2 has been executed by the
Parties to be effective as of the Amendment No. 2 Effective Date.






*Confidential Treatment Requested. 
Omitted portions filed with the Commission.



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  CARDINAL HEALTH PTS, LLC

  	
   

  	
  CUBIST PARMACEUTICALS, INC.

  
	
   

  	
   

  	
   

  
	
  By:

  	
   

  	
  /s/ Shawn L. Gallagher

  	
   

  	
   

  	
  By:

  	
   

  	
  /s/ Lindon M. Fellows

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  
	
  Name:

  	
   

  	
  Shawn L.
  Gallagher

  	
   

  	
   

  	
  Name:

  	
   

  	
  Lindon M.
  Fellows

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  
	
  Title:

  	
   

  	
  VP and General
  Manager

  	
   

  	
   

  	
  Title:

  	
   

  	
  Senior Vice
  President

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
  Technical
  Operations

  	
   

  



 



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EXHIBIT B-1


[]*






*Confidential Treatment
Requested.  Omitted portions filed with
the Commission.



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