Exhibit 10.61  Cubist Pharmaceuticals, Inc. Director Compensation, Benefits, Programs (Effective as of June 4, 2009)  Director
Compensation  Element
  
  CompensationRetainer
  
  Non-Executive
  Chair of the Board - $34,000
  Lead Director -
  $28,000
  Other Non-Employee
  Directors - $22,000
  Paid on an
  annual basis in June in either cash or stock; cash/stock election to be
  made at March board meeting; pro rated based on number of months served
  during the 12 months beginning on the date of the prior calendar years Annual
  Meeting of StockholdersInitial Option
  Grant
  
  Non-Executive Chair of the Board: Stock options with
  a Black-Scholes value of $250,000
  
  Lead Director: 
  Stock options with a Black-Scholes value of $200,000
  
  Other Non-Employee Directors: Stock options with a
  Black-Scholes value of $150,000
  
  Grant
  Date/vesting: Vests quarterly on a pro rata basis over 3 years from the grant
  dateAnnual Option
  Grant
  
  Non-Executive Chair of the Board: Stock options with
  a Black-Scholes value of $250,000
  
  Lead Director: 
  Stock options with a Black-Scholes value of $200,000
  
  Other Non-Employee Directors: Stock options with a
  Black-Scholes value of $150,000
  
  Grant Date/vesting: Options will be granted (and
  valued) on the date of each Annual Meeting of Stockholders; vests 100% on the
  earlier of the first anniversary of the grant date or the date of the next
  calendar years Annual Meeting of StockholdersMeeting Fee - Board Meetings
  
  $4,000 per meeting attended (in person) (except for
  Non-Executive Chair of the Board and Lead Director, see below)
  
  $1,000 per meeting attended (by phone) (except for
  Non-Executive Chair of the Board and Lead Director, see below)Meeting Fee - Committee Meetings (non-Chair members)
  
  Audit Committee: $2,000 per meeting attended (in
  person or by phone)
  
  Other Committees (including Special Committees):
  $1,500 per meeting attended (in person or by phone)Meeting Fee -
  
  Audit Committee: $4,000 per meeting led (in person
  or by phone)


Committee Chairs
  
  Other Committees (including Special Committees):
  $3,500 per meeting led (in person or by phone)Meeting Fee  Board Meetings - Non-Executive Chair
  of the Board
  
  $5,000 per Board Meeting led (in person)
  $2,000 per meeting led (by phone)Meeting Fee  Board Meeting - Lead Director
  
  $5,000 per Board Meeting led (in person)
  
  $2,000 per meeting led (by phone)Meeting Fee 
  Non-Committee Members Attending Committee Meetings
  
  Paid the same per meeting fee as a non-Chair member
  of the Committee  Director Benefits  Expense Reimbursement
  
  Cubist shall
  reimburse the cost of all reasonable travel related expenses and meals
  incurred in connection with attending Board or Committee Meetings.  Directors should travel one class below
  first class. Exceptions will be handled on a case-by-case basis and should be
  submitted to the Chair (or, if there is no Chair, the Lead Director)D & O
  Insurance
  
  Cubist provides
  Director & Officer Insurance for all Board Members.NACD Membership
  
  Cubist provides
  a membership to the National Association of Corporate Directors for all Board
  MembersDirector Education
  Programs
  
  Cubist supports
  director education and will reimburse directors for reasonable expenses
  incurred in connection with participation in director education
  programs.  Directors are expected to
  report all such participation to the Secretary of the Corporation.  Cubist also provides in-house direction
  education and has a Director Orientation Program.  Administration  1.Cubist delivers a check at each regularly scheduled
in-person Board Meeting that includes compensation for all Board and Committee
meetings attended since the last regularly scheduled in-person Board
Meeting.  Included with the check is an
Attendance Report and Stock Option Report. 
Directors are compensated for Board or Committee meetings designated by
the Chairman of the Board, Lead Director, or Committee Chairs, as the case may
be, for which minutes are prepared.  2.Board retainer is payable on an annual basis as of the
date of the Annual Meeting of Stockholders


in either cash or stock,
in recognition of the previous 12 months of service beginning on the date of
the previous calendar years Annual Meeting of Stockholders. Stock or cash
election will be made in March. The retainer shall be pro-rated based on the
number of months served as a Director in the previous 12 months.  3.Receipts must be submitted to Cubists CEO within 60
days of each travel engagement.  4.A summary of Cubist Director & Officers Insurance
Policy is included in the Directors Handbook.