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                                                                    Exhibit 99.4

                          CUBIST PHARMACEUTICALS, INC.

                              AMENDED AND RESTATED
                         CORPORATE GOVERNANCE GUIDELINES
                          EFFECTIVE SEPTEMBER 15, 2003

                                TABLE OF CONTENTS

<Table>
                                                                          

1.    ROLE OF THE BOARD AND MANAGEMENT..........................................2
2.    SELECTION OF CHAIRMAN, CEO AND LEAD DIRECTOR..............................2
3.    NUMBER OF COMMITTEES......................................................2
4.    ASSIGNMENT AND ROTATION OF COMMITTEE MEMBERS..............................2
5.    COMMITTEE AGENDA..........................................................3
6.    SELECTION OF AGENDA ITEMS FOR THE BOARD MEETINGS..........................3
7.    BOARD MATERIALS DISTRIBUTED IN ADVANCE....................................3
8.    REGULAR ATTENDANCE OF NON-DIRECTORS AT BOARD MEETINGS.....................3
9.    EXECUTIVE SESSIONS OF THE BOARD...........................................3
10.   BOARD ACCESS TO SENIOR MANAGEMENT.........................................4
11.   BOARD COMPENSATION REVIEW.................................................4
12.   SIZE OF THE BOARD; ATTENDANCE.............................................4
13.   INDEPENDENT DIRECTORS.....................................................4
14.   DEFINITION OF INDEPENDENCE................................................4
15.   FORMER CEO'S BOARD MEMBERSHIP.............................................4
16.   BOARD MEMBERSHIP CRITERIA.................................................5
17.   SELECTION OF NEW DIRECTOR CANDIDATES......................................5
18.   ASSESSING THE BOARD'S PERFORMANCE.........................................5
19.   DIRECTORS WHO CHANGE THEIR PRESENT JOB RESPONSIBILITY.....................5
20.   TERM LIMITS...............................................................6
21.   RETIREMENT AGE............................................................6
22.   FORMAL EVALUATION OF THE CEO..............................................6
23.   SUCCESSION PLANNING.......................................................6
24.   MANAGEMENT DEVELOPMENT....................................................7
25.   BOARD INTERACTION WITH INVESTORS, THE PRESS, CUSTOMERS, ETC...............7
26.   SHARE OWNERSHIP OF DIRECTORS..............................................7
27.   CONFLICTS OF INTEREST.....................................................7
28.   DIRECTOR CONTINUING EDUCATION.............................................7
29.   CONSULTING AGREEMENTS WITH DIRECTORS......................................7
30.   DONATIONS TO DIRECTORS OR OFFICER CHARITIES...............................8
31.   MEMBERSHIP ON OTHER BOARDS................................................8
</Table>

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                          CUBIST PHARMACEUTICALS, INC.

                              AMENDED AND RESTATED
                         CORPORATE GOVERNANCE GUIDELINES
                          EFFECTIVE SEPTEMBER 15, 2003

1.   ROLE OF THE BOARD AND MANAGEMENT

     The Board's fundamental responsibility is to represent the interests of the
stockholders of Cubist Pharmaceuticals, Inc. (the "Company"). In fulfilling its
responsibilities, the Board performs the following principal functions: (i)
selecting, evaluating, compensating and, where necessary, replacing the CEO and
other executive officers; (ii) approving corporate strategy, annual operating
budgets, mergers and acquisitions and significant financings; (iii) providing
general oversight of the business; (iv) evaluating and establishing Board
processes, performance and compensation; (v) selecting Directors; and (vi)
monitoring legal and ethical conduct. These activities are performed in
cooperation with the CEO.

     Management executes the approved plans and budgets and is responsible for
the day-to-day management of the Company.

2.   SELECTION OF CHAIRMAN, CEO, AND LEAD DIRECTOR

     The Board has the sole responsibility to select its Chairman and the CEO.
The Board shall also consider, upon recommendation from the Corporate Governance
Committee, appointing a Lead Director if the Chairman and CEO positions are held
by the same individual. The Chairman shall have the responsibility for managing
the Board. The CEO shall have the responsibility for managing the Company. The
Lead Director, if any, shall have the responsibility for leading meetings of the
independent directors and shall serve as a liaison between independent directors
and the CEO if the CEO is also the Chairman. If the Chairman and CEO positions
are not held by the same individual, the CEO need not be a member of the Board.

3.   NUMBER OF COMMITTEES

     The current three committees of the Board are Audit, Compensation and
Corporate Governance. From time to time, AD HOC committees may be established
for special assignments.

4.   ASSIGNMENT AND ROTATION OF COMMITTEE MEMBERS

     The Corporate Governance Committee is responsible, with consideration of
the recommendations of the Chairman, the CEO, and individual Board members, for
recommending Board members to individual committees. In making such

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recommendation, the Corporate Governance Committee will take into consideration
individual skill sets and preferences as well as any requirements of committee
charters.

     Consideration will be given to rotating committee members each year. To the
extent practical, the Corporate Governance Committee will endeavor to rotate one
person on and one person off each committee each year. In addition, to the
extent practical, the Corporate Governance Committee will endeavor to rotate
committee chairmen every two to five years, with the expectation that a new
chairman will have served on the committee for no less than one year before
becoming chairman of said committee.

5.   COMMITTEE AGENDA

     The Chairman of each committee, in consultation with the appropriate
members of Management and staff, will develop the committee's agenda.

     Each committee will issue a schedule of agenda subjects to be discussed for
the ensuing meeting (to the degree that these can be foreseen).

6.   SELECTION OF AGENDA ITEMS FOR BOARD MEETINGS

     The Chairman, in consultation with management, establishes the agenda for
each Board meeting. Directors may add topics to the agenda. The Chairman may
solicit from Board members any additional items they feel should be covered.

7.   BOARD MATERIALS DISTRIBUTED IN ADVANCE

     Information and data that is important to the Board's understanding of the
business is distributed in writing to the Board before the Board meets.
Management will see that this material is as concise as possible while still
providing the desired information.

     As a general rule, presentations on specific subjects will be sent to
the Board members in advance so that the Board meeting time may be conserved,
and discussion time focused on questions that the Board has about the material.

8.   REGULAR ATTENDANCE OF NON-DIRECTORS AT BOARD MEETINGS

     The Board is comfortable with regular attendance at each Board meeting of
non-board members who are invited by the Chairman, except during Executive
Sessions of the Board.

9.   EXECUTIVE SESSIONS OF THE BOARD

     The Board shall regularly conduct Executive Sessions of the Board without
the members of Management present.

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10.  BOARD ACCESS TO SENIOR MANAGEMENT

     Board members have complete access to Management.

     Furthermore, the Board encourages Management to, from time to time, bring
managers into Board meetings who (a) can provide additional insight to the items
being discussed because of personal involvement in these areas, and/or (b)
represent managers with executive potential that the Management believes should
be given exposure to the Board.

11.  BOARD COMPENSATION REVIEW

     The CEO should report, from time to time to the Compensation Committee the
status of Board compensation in relation to other like companies. Changes in
Board compensation, if any, should come at the recommendation of the
Compensation Committee, but with discussion and approval of the full Board.

12.  SIZE OF THE BOARD; ATTENDANCE

     The Board should consider the appropriate size of the Board and fix the
number of Directors pursuant to a resolution adopted by a majority of the Board.
The Board believes that Directors, to the extent possible, should: (a) attend
all Board meetings and all applicable committee meetings, in person or by phone,
and in no event should a Director attend less than 75% of Board meetings or
applicable Committee meetings and (b) participate in the entire meeting. If a
Director attends a Board Meeting via telephone, such Director shall use a land
line (I.E., not a cell phone) unless this requirement is waived by the Chairman.

13.  INDEPENDENT DIRECTORS

     A majority of Directors on the Board will be Independent Directors. (See
Item 14 for Definition of Independence)

14.  DEFINITION OF INDEPENDENCE

     An independent Director is one who is independent of Management and free
from any relationship that, in the opinion of the Corporate Governance
Committee, would interfere with the exercise of independent judgment as a
Director and who meets the definition of independence set forth in applicable
SEC and Nasdaq regulations.

15.  FORMER CEO'S BOARD MEMBERSHIP

     It is assumed that when a CEO resigns from that position, he should offer
his resignation from the Board at the same time. Whether or not the individual
continues to serve on the Board is a matter for discussion with the new CEO and
the Board.

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     A former CEO or any other former officer serving on the Board will not be
considered independent until the expiration of any applicable "cooling off
period" and he/she meets the definition of independence set forth in applicable
SEC and Nasdaq regulations.

16.  BOARD MEMBERSHIP CRITERIA

     The Corporate Governance Committee is responsible for reviewing with the
Board, on an annual basis, the appropriate skills and characteristics required
of Board members in the context of the current make-up of the Board.

17.  SELECTION OF NEW DIRECTOR CANDIDATES

     The Board is responsible for selecting new members to join the Board and
will either elect such new member to fill a vacant seat or recommend such new
member to the shareholders for election at an Annual Meeting of Stockholders .
The Board delegates the screening process involved to the Corporate Governance
Committee with the direct input from the Chairman, the CEO, and such other
executive officers as the Corporate Governance Committee deems appropriate. New
Directors will participate in an orientation program, including visits to
Company facilities and discussions with executive officers.

18.  ASSESSING THE BOARD'S PERFORMANCE

     The Corporate Governance Committee is responsible to report to the Board,
on an annual basis, an assessment of the Board's performance and procedures.
This will be discussed by the full Board.

     This assessment is of the Board's contribution as a whole and specifically
reviews areas in which the Board and/or Management believes a better
contribution could be made. Its purpose is to increase the effectiveness of the
Board, not to review individual Board members.

     In addition, the Corporate Governance Committee will review the performance
of each individual Board member prior to proposing him or her for re-election.

19.  DIRECTORS WHO CHANGE THEIR PRESENT JOB RESPONSIBILITY

     It is the sense of the Board that individual Directors who change the
full-time, non-Cubist responsibility they held when they were elected to the
Board should volunteer to resign from the Board.

     It is not the sense of the Board, however, that the Directors who retire or
change from the position they held when they came on the Board should
necessarily leave the Board. Therefore, there should be an opportunity for the
full Board, after preliminary

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review by the Corporate Governance Committee, to review the continued
appropriateness of Board membership under these circumstances.

20.  TERM LIMITS

     Directors currently serve for three (3) year terms. While term limits could
help ensure that there are fresh ideas and viewpoints available to the Board,
they hold the disadvantage of losing the contribution of Directors who have been
able to develop, over a period of time, increasing insight into the Company and
its operations and, therefore, provide an increasing contribution to the Board
as a whole. Therefore, Directors shall be expected to serve for no more than
three (3) terms unless, upon recommendation of the Corporate Governance
Committee, the Board shall approve additional terms.

21.  RETIREMENT AGE

     It is the sense of the Board that Directors will volunteer to resign from
the Board at the end of the term during which they reach the age of 72. While a
retirement age could help ensure that there are fresh ideas and viewpoints
available to the Board, it holds the disadvantage of losing the contribution of
Directors who have been able to develop, over a period of time, increasing
insight into the Company and its operations and, therefore, provide an
increasing contribution to the Board as a whole. Therefore, Directors shall be
expected to resign from the Board at the end of the term during which they reach
the age of 72 unless, upon recommendation of the Corporate Governance Committee,
the Board shall approve additional terms.

22.  FORMAL EVALUATION OF THE CEO

     The Compensation Committee will submit to the Board annually at the close
of the fiscal year an evaluation of the CEO. After agreement of the evaluation
by the Independent Directors, the evaluation will be communicated to the CEO by
the Chairman of the Compensation Committee. The evaluation will be based on
objective criteria, communicated to the CEO at the beginning of each fiscal
year, including performance of the business, accomplishment of near and long
term objectives, development of Management, ETC. The evaluation will be used by
the Compensation Committee when considering the compensation of the CEO.

23.  SUCCESSION PLANNING

     There will be available, on a continuing basis, the CEO's recommendation as
to his or her successor should he or she be unexpectedly disabled.

     There will be an annual report by the CEO to the Board on succession
planning.

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24.  MANAGEMENT DEVELOPMENT

     In addition to the succession planning annual report, the CEO will at the
same time report on Management development to the Board.

     In addition, the CEO reviews annually with the Compensation Committee
performance of the other executive officers and the extent to which these
officers have accomplished their goals. The Compensation Committee may, in turn,
provide a summary of these reports and reviews to the full Board.

25.  BOARD INTERACTION WITH INVESTORS, THE PRESS, CUSTOMERS. ETC.

     Management speaks for the Company. Directors do not speak for the Company.

26.  SHARE OWNERSHIP OF DIRECTORS

     The Board believes that Directors will be stockholders and have a financial
stake in the Company. It is anticipated that each Director will develop a
meaningful ownership position in the Company over time, depending upon
individual circumstances. All Directors will comply with the Company's Equity
Interest Policy.

27.  CONFLICTS OF INTEREST

     A Director's business or family relationships may occasionally give rise to
that Director's material personal interest on a particular issue. Each Director
is responsible for disclosing situations that he or she reasonably believes give
rise to a potential conflicts of interest to the Corporate Governance Committee.
In addition, the Corporate Governance Committee shall ask Directors about
potential conflicts of interest at least once per year. The Board, upon
recommendation of the Corporate Governance Committee and after consultation with
the Company's outside counsel, determines on a case-by-case basis whether such a
conflict of interest exists. The Board takes appropriate steps to identify such
potential conflicts and to assure that all Directors voting on an issue are
disinterested with respect to that issue.

28.  DIRECTOR CONTINUING EDUCATION

     The Board encourages Directors to participate in continuing education
programs, including, but not limited to, those recommended by the Corporate
Governance Committee.

29.  CONSULTING AGREEMENT WITH DIRECTORS

     The Company shall not enter into any consulting agreement with any Director
without the prior approval of the Board.

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30.  DONATIONS TO DIRECTOR OR OFFICER CHARITIES

     Except for any contributions made pursuant to a company matching program
that is generally available to all employees, the Company shall not make any
donation to any charity with which any Director or Officer is affiliated without
the prior approval of the Board.

31.  MEMBERSHIP ON OTHER BOARDS

     From time to time, Directors, Officers, or other employees may wish to
serve on the boards of other public, private, or non-profit organizations. Such
service is often in the best interests of both the Company and the individual,
but the Company has a legitimate interest in protecting against conflicts of
interest and limiting demands on employee's time. Therefore, the following
procedures shall apply:

          1).  if a director intents to join a board, he or she shall so notify
               the Corporate Governance Committee, carbon copying the Company
               Secretary.

          2).  if a Section 16 Officer wishes to join a board, he or she shall
               not do so without prior approval of the Board.

          3).  if (a) an officer who is not a Section 16 Officer, or (b) a
               non-officer employee wishes to joint a board, he or she shall not
               do so without prior approval of the CEO.

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