Document:

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                                                                    EXHIBIT 10.3

          UNLESS THIS CERTIFICATE IS PRESENTED BY AN AUTHORIZED REPRESENTATIVE
OF THE DEPOSITORY TRUST COMPANY, A NEW YORK CORPORATION ("DTC"), TO THE COMPANY
OR ITS AGENT FOR REGISTRATION OF TRANSFER, EXCHANGE OR PAYMENT, AND ANY
CERTIFICATE ISSUED IS REGISTERED IN THE NAME OF CEDE & CO. OR IN SUCH OTHER NAME
AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF THE DEPOSITORY TRUST COMPANY
(AND ANY PAYMENT HEREON IS MADE TO CEDE & CO. OR TO SUCH OTHER ENTITY AS IS
REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC), ANY TRANSFER, PLEDGE OR OTHER
USE HEREOF FOR VALUE OR OTHERWISE BY OR TO ANY PERSON IS WRONGFUL INASMUCH AS
THE REGISTERED OWNER HEREOF, CEDE & CO., HAS AN INTEREST HEREIN. THIS NOTE IS A
GLOBAL NOTE WITHIN THE MEANING OF THE INDENTURE HEREINAFTER REFERRED TO AND IS
REGISTERED IN THE NAME OF A DEPOSITARY OR A NOMINEE THEREOF. THIS NOTE IS
EXCHANGEABLE FOR SECURITIES REGISTERED IN THE NAME OF A PERSON OTHER THAN THE
DEPOSITARY OR ITS NOMINEE ONLY IN THE LIMITED CIRCUMSTANCES DESCRIBED IN THE
INDENTURE AND, UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR
SECURITIES IN DEFINITIVE FORM, THIS NOTE MAY NOT BE TRANSFERRED EXCEPT AS A
WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE
DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE OF THE DEPOSITARY OR BY THE
DEPOSITARY OR ANY SUCH NOMINEE TO A SUCCESSOR DEPOSITARY OR A NOMINEE OF SUCH
SUCCESSOR DEPOSITARY.

          THIS NOTE (OR ITS PREDECESSOR) WAS ORIGINALLY ISSUED IN A TRANSACTION
EXEMPT FROM REGISTRATION UNDER THE UNITED STATES SECURITIES ACT OF 1933 (THE
"SECURITIES ACT"), AND THIS NOTE AND THE COMMON STOCK ISSUABLE UPON CONVERSION
THEREOF MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED IN THE ABSENCE OF SUCH
REGISTRATION OR AN APPLICABLE EXEMPTION THEREFROM. EACH PURCHASER OF THIS NOTE
IS HEREBY NOTIFIED THAT THE SELLER OF THIS NOTE MAY BE RELYING ON THE EXEMPTION
FROM THE PROVISIONS OF SECTION 5 OF THE SECURITIES ACT PROVIDED BY RULE 144A
THEREUNDER.

          THE HOLDER OF THIS NOTE AGREES FOR THE BENEFIT OF THE COMPANY THAT (A)
THIS NOTE AND THE NOTE COMMON STOCK ISSUABLE UPON CONVERSION THEREOF MAY BE
OFFERED, RESOLD, PLEDGED OR OTHERWISE TRANSFERRED, ONLY (I) IN THE UNITED STATES
TO A PERSON WHOM THE SELLER REASONABLY BELIEVES IS A QUALIFIED INSTITUTIONAL
BUYER (AS DEFINED IN RULE 144A UNDER THE SECURITIES ACT) IN A TRANSACTION
MEETING THE REQUIREMENTS OF RULE 144A, (II) OUTSIDE THE UNITED STATES IN AN
OFFSHORE TRANSACTION IN ACCORDANCE WITH RULE 904 UNDER THE

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                                      -2-

SECURITIES ACT, (III) PURSUANT TO AN EXEMPTION FROM REGISTRATION UNDER THE
SECURITIES ACT PROVIDED BY RULE 144 THEREUNDER (IF AVAILABLE) OR (IV) PURSUANT
TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT, IN EACH OF
CASES (I) THROUGH (IV) IN ACCORDANCE WITH ANY APPLICABLE SECURITIES LAWS OF ANY
STATE OF THE UNITED STATES, AND (B) THE HOLDER WILL, AND EACH SUBSEQUENT HOLDER
IS REQUIRED TO, NOTIFY ANY PURCHASER OF THIS NOTE FROM IT OF THE RESALE
RESTRICTIONS REFERRED TO IN (A) ABOVE. IN ANY CASE, THE HOLDER HEREOF WILL NOT,
DIRECTLY OR INDIRECTLY, ENGAGE IN ANY HEDGING TRANSACTIONS WITH REGARD TO THE
NOTES EXCEPT AS PERMITTED UNDER THE SECURITIES ACT.

          THE HOLDER OF THIS NOTE IS ENTITLED TO THE BENEFITS OF A REGISTRATION
RIGHTS AGREEMENT (AS SUCH TERM IS DEFINED IN THE INDENTURE REFERRED TO IN THE
NOTE) AND, BY ITS ACCEPTANCE HEREOF, AGREES TO BE BOUND BY AND TO COMPLY WITH
THE PROVISIONS OF SUCH REGISTRATION RIGHTS AGREEMENT.

          THIS NOTE MAY NOT BE SOLD OR TRANSFERRED TO, AND EACH PURCHASER BY ITS
PURCHASE OF THIS SECURITY SHALL BE DEEMED TO HAVE REPRESENTED AND COVENANTED
THAT IT IS NOT ACQUIRING THIS SECURITY FOR OR ON BEHALF OF, AND WILL NOT
TRANSFER THIS SECURITY TO, ANY PENSION OR WELFARE PLAN AS DEFINED IN SECTION 3
OF THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974, AS AMENDED ("ERISA")
EXCEPT THAT SUCH PURCHASE FOR OR ON BEHALF OF A PENSION OR WELFARE PLAN SHALL BE
PERMITTED:

                  (1.)    TO THE EXTENT SUCH PURCHASE IS MADE BY OR ON BEHALF
          OF A BANK COLLECTIVE INVESTMENT FUND MAINTAINED BY THE PURCHASER IN
          WHICH NO PLAN (TOGETHER WITH ANY OTHER PLANS MAINTAINED BY THE SAME
          EMPLOYER OR EMPLOYEE ORGANIZATION) HAS AN INTEREST IN EXCESS OF 10% OF
          THE TOTAL ASSETS IN SUCH COLLECTIVE INVESTMENT FUND, AND THE OTHER
          APPLICABLE CONDITIONS OF PROHIBITED TRANSACTION CLASS EXEMPTION 91-38
          ISSUED BY THE DEPARTMENT OF LABOR ARE SATISFIED;

                  (2.)    TO THE EXTENT SUCH PURCHASE IS MADE BY OR ON BEHALF OF
          AN INSURANCE COMPANY POOLED SEPARATE ACCOUNT MAINTAINED BY THE
          PURCHASER IN WHICH, AT ANY TIME WHILE THESE SECURITIES ARE
          OUTSTANDING, NO PLAN (TOGETHER WITH ANY OTHER PLANS MAINTAINED BY THE
          SAME EMPLOYER OR EMPLOYEE ORGANIZATION) HAS AN INTEREST IN EXCESS OF
          10% OF THE TOTAL OF ALL ASSETS IN SUCH POOLED SEPARATE ACCOUNT, AND
          THE OTHER APPLICABLE CONDITIONS OF PROHIBITED TRANSACTION CLASS
          EXEMPTION 90-1 ISSUED BY THE DEPARTMENT OF LABOR ARE SATISFIED;

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                                      -3-

                  (3.)    TO THE EXTENT SUCH PURCHASE IS MADE ON BEHALF OF A
          PLAN BY (A) AN INVESTMENT ADVISER REGISTERED UNDER THE INVESTMENT
          ADVISERS ACT OF 1940, AS AMENDED (THE "1940 ACT"), THAT HAD AS OF THE
          LAST DAY OF ITS MOST RECENT FISCAL YEAR TOTAL ASSETS UNDER ITS
          MANAGEMENT AND CONTROL IN EXCESS OF $50.0 MILLION AND HAD
          STOCKHOLDERS' OR PARTNERS' EQUITY IN EXCESS OF $750,000, AS SHOWN IN
          ITS MOST RECENT BALANCE SHEET PREPARED IN ACCORDANCE WITH GENERALLY
          ACCEPTED ACCOUNTING PRINCIPLES, OR (B) A BANK AS DEFINED IN SECTION
          202(A)(2) OF THE 1940 ACT WITH EQUITY CAPITAL IN EXCESS OF $1.0
          MILLION AS OF THE LAST DAY OF ITS MOST RECENT FISCAL YEAR, OR (C) AN
          INSURANCE COMPANY WHICH IS QUALIFIED UNDER THE LAWS OF MORE THAN ONE
          STATE TO MANAGE, ACQUIRE OR DISPOSE OF ANY ASSETS OF A PENSION OR
          WELFARE PLAN, WHICH INSURANCE COMPANY HAS AS OF THE LAST DAY OF ITS
          MOST RECENT FISCAL YEAR, NET WORTH IN EXCESS OF $1.0 MILLION AND WHICH
          IS SUBJECT TO SUPERVISION AND EXAMINATION BY A STATE AUTHORITY HAVING
          SUPERVISION OVER INSURANCE COMPANIES AND, IN ANY CASE, SUCH INVESTMENT
          ADVISER, BANK OR INSURANCE COMPANY IS OTHERWISE A QUALIFIED
          PROFESSIONAL ASSET MANAGER, AS SUCH TERM IS USED IN PROHIBITED
          TRANSACTION CLASS EXEMPTION 84-14 ISSUED BY THE DEPARTMENT OF LABOR,
          AND THE ASSETS OF SUCH PLAN WHEN COMBINED WITH THE ASSETS OF OTHER
          PLANS ESTABLISHED OR MAINTAINED BY THE SAME EMPLOYER (OR AFFILIATE
          THEREOF) OR EMPLOYEE ORGANIZATION AND MANAGED BY SUCH INVESTMENT
          ADVISER, BANK OR INSURANCE COMPANY, DO NOT REPRESENT MORE THAN 20% OF
          THE TOTAL CLIENT ASSETS MANAGED BY SUCH INVESTMENT ADVISER, BANK OR
          INSURANCE COMPANY AT THE TIME OF THE TRANSACTION, AND THE OTHER
          APPLICABLE CONDITIONS OF SUCH EXEMPTION ARE OTHERWISE SATISFIED;

                  (4.)    TO THE EXTENT SUCH PLAN IS A GOVERNMENTAL PLAN (AS
          DEFINED AS SECTION 3 OF ERISA) WHICH IS NOT SUBJECT TO THE PROVISIONS
          OF TITLE 1 OF ERISA OR SECTION 401 OF THE INTERNAL REVENUE CODE OF
          1986, AS AMENDED (THE "CODE");

                  (5.)    TO THE EXTENT SUCH PURCHASE IS MADE BY OR ON BEHALF OF
          AN INSURANCE COMPANY USING THE ASSETS OF ITS GENERAL ACCOUNT, THE
          RESERVES AND LIABILITIES FOR THE GENERAL ACCOUNT CONTRACTS HELD BY OR
          ON BEHALF OF ANY PLAN, TOGETHER WITH ANY OTHER PLANS MAINTAINED BY THE
          SAME EMPLOYER (OR ITS AFFILIATES) OR EMPLOYEE ORGANIZATION, DO NOT
          EXCEED 10% OF THE TOTAL RESERVES AND LIABILITIES OF THE INSURANCE
          COMPANY GENERAL

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          ACCOUNT (EXCLUSIVE OF SEPARATE ACCOUNT LIABILITIES), PLUS SURPLUS AS
          SET FORTH IN THE NATIONAL ASSOCIATION OF INSURANCE COMMISSIONERS
          ANNUAL STATEMENT FILED WITH THE STATE OF DOMICILE OF THE INSURER, IN
          ACCORDANCE WITH PROHIBITED TRANSACTION CLASS EXEMPTION 95-60, AND THE
          OTHER APPLICABLE CONDITIONS OF SUCH EXEMPTION ARE OTHERWISE SATISFIED;

                  (6.)    TO THE EXTENT PURCHASE IS MADE BY AN IN-HOUSE ASSET
          MANAGER WITHIN THE MEANING OF PART IV(A) OF PROHIBITED TRANSACTION
          CLASS EXEMPTION 96-23, SUCH MANAGER HAS MADE OR PROPERLY AUTHORIZED
          THE DECISION FOR SUCH PLAN TO PURCHASE THIS SECURITY, UNDER
          CIRCUMSTANCES SUCH THAT PROHIBITED TRANSACTION CLASS EXEMPTION 96-23
          IS APPLICABLE TO THE PURCHASE AND HOLDING OF THIS SECURITY; OR

                  (7.)    TO THE EXTENT SUCH PURCHASE WILL NOT OTHERWISE GIVE
          RISE TO A TRANSACTION  DESCRIBED IN SECTION 406 OR SECTION  4975(C)(1)
          OF THE CODE FOR  WHICH A  STATUTORY  OR  ADMINISTRATIVE  EXEMPTION  IS
          UNAVAILABLE.

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                          CUBIST PHARMACEUTICALS, INC.

CUSIP: 229678 AA5                                                            R-1

                 5 1/2% CONVERTIBLE SUBORDINATED NOTES DUE 2008

          Cubist Pharmaceuticals, Inc., a Delaware corporation (the "Company",
which term shall include any successor corporation under the Indenture referred
to in the Note), promises to pay to Cede & Co., or its registered assigns, the
principal sum of One Hundred and Twenty-Five Million Dollars ($125,000,000) on
November 1, 2008 or such greater or lesser amount as is indicated on the
Schedule of Exchanges of Notes on the Note.

          Interest Payment Dates: November 1 and May 1

          Record Dates: October 15 and April 15

          This Note is convertible as specified below. Additional provisions of
this Note are set forth below.

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                                       -2-

          IN WITNESS WHEREOF, the Company has caused this instrument to be duly
executed.

                                             Cubist Pharmaceuticals, Inc.

                                             By:  /s/ THomas A. Shea
                                                 -------------------------------
                                             Name: Thomas A. Shea
                                             Title:  CFO
Attest:

By:    /s/ Michael V. Greco
    ----------------------------------
Name:  Michael V. Greco
Title:

Dated:   October 26, 2001

Trustee's Certificate of Authentication: This is one of the Notes referred to in
the within-mentioned Indenture.

THE BANK OF NEW YORK,
as Trustee

By:      /s/ Kisha Holder
    ----------------------------------
Name:  Kisha Holder
Title: Assistant Treasurer

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                          CUBIST PHARMACEUTICALS, INC.
                 5 1/2% CONVERTIBLE SUBORDINATED NOTES DUE 2008

1.        INTEREST

          Cubist Pharmaceuticals, Inc., a Delaware corporation (the "Company",
which term shall include any successor corporation under the Indenture
hereinafter referred to), promises to pay interest on the principal amount of
this Note at the rate of 5 1/2% per annum. The Company shall pay interest
semiannually on November 1 and May 1 of each year, commencing May 1, 2002,
unless such date is not a business day, in which case, the Company shall pay
interest on the next succeeding business day and such payment shall be deemed to
have been paid on such interest payment date and no interest shall accrue during
the additional period of time. Interest on the Notes shall accrue from the most
recent date to which interest has been paid or, if no interest has been paid,
from October 26, 2001; provided, however, that if there is not an existing
default in the payment of interest and if this Note is authenticated between a
record date referred to on the face hereof and the next succeeding interest
payment date, interest shall accrue from such interest payment date. Interest
will be computed on the basis of a 360-day year of twelve 30-day months. Any
reference herein to interest accrued or payable as of any date shall include any
Additional Interest accrued or payable on such date as provided in the
Registration Rights Agreement.

2.        METHOD OF PAYMENT

          The Company shall pay interest on this Note (except defaulted
interest) to the person who is the Holder of this Note at the close of business
on October 15 or April 15, as the case may be, next preceding the related
interest payment date. The Holder must surrender this Note to a Paying Agent to
collect payment of principal. The Company will pay principal and interest in
money of the United States that at the time of payment is legal tender for
payment of public and private debts. The Company may, however, pay principal and
interest in respect of any Definitive Note by check or wire payable in such
money; provided, however, that a Holder with an aggregate principal amount in
excess of $2,000,000 will be paid by wire transfer in immediately available
funds at the election of such Holder. The Company may mail an interest check to
the Holder's registered address. Notwithstanding the foregoing, so long as this
Note is registered in the name of a Depositary or its nominee, all payments
hereon shall be made by wire transfer of immediately available funds to the
account of the Depositary or its nominee.

3.        PAYING AGENT, REGISTRAR AND CONVERSION AGENT

          Initially, the Bank of New York (the "Trustee," which term shall
include any successor trustee under the Indenture hereinafter referred to) will
act as Paying Agent, Registrar and Conversion Agent. The Company may change any
Paying Agent, Registrar or Conversion Agent without notice to the Holder. The
Company or any of its Subsidiaries may, subject to certain limitations set forth
in the Indenture, act as Paying Agent or Registrar.

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4.        INDENTURE, LIMITATIONS

          This Note is one of a duly authorized issue of Notes of the Company
designated as its 5 1/2% Convertible Subordinated Notes due 2008 (the "Notes"),
issued under an Indenture dated as of October 26, 2001 (together with any
supplemental indentures thereto, the "Indenture"), between the Company and the
Trustee. The terms of this Note include those stated in the Indenture and those
required by or made part of the Indenture by reference to the Trust Indenture
Act of 1939, as amended, as in effect on the date of the Indenture. This Note is
subject to all such terms, and the Holder of this Note is referred to the
Indenture and said Act for a statement of them. All capitalized terms used but
not defined herein shall have the meaning ascribed to such term in the
Indenture.

          The Notes are subordinated unsecured obligations of the Company
limited to $175,000,000 aggregate principal amount (taking into account the
45-day option granted to the initial purchasers of the Notes to purchase up to
an additional $50,000,000 in aggregate principal amount of Notes), subject to
Section 2.2 of the Indenture. The Indenture does not limit other debt of the
Company, secured or unsecured, including Senior Indebtedness.

5.        PROVISIONAL AND OPTIONAL REDEMPTION

          The Notes may be redeemed at the election of the Company, as a whole
or in part from time to time, at any time prior to November 3, 2004 (a
"PROVISIONAL REDEMPTION"), upon at least 20 and not more than 60 days' notice by
mail to the Holders of the Notes at a redemption price equal to $1,000 per
$1,000 principal amount of the Notes redeemed plus accrued and unpaid interest,
if any (such amount, together with the Make-Whole Payment described below, the
"PROVISIONAL REDEMPTION PRICE"), to but excluding the date of redemption (the
"PROVISIONAL REDEMPTION DATE") if (1) the Closing Sale Price of the Common Stock
has exceeded 150% of the Conversion Price for at least 20 trading days within a
period of any 30 consecutive trading days ending on the trading day prior to the
date of mailing of the notice of Provisional Redemption (the "NOTICE DATE"), and
(2) a shelf registration statement covering resales of the Notes and the Common
Stock issuable upon conversion thereof is effective and available for use and is
expected to remain effective and available for use for the 30 days following the
Provisional Redemption Date unless registration is no longer required.

          Upon any such Provisional Redemption, the Company, shall make an
additional payment, at its option, in cash or Common Stock or a combination of
cash and Common Stock (the "MAKE-WHOLE PAYMENT") with respect to the Notes
called for redemption to holders on the Notice Date in an amount equal to $165
per $1,000 principal amount of the Notes, less the amount of any interest
actually paid (including, if the Provisional Redemption Date occurs after a
record date but before an interest payment date, any interest paid or payable in
connection with such interest payment date) on such Notes on or prior to the
Provisional Redemption Date. Payments made in Common Stock will be valued at 97%
of the average closing sales prices of Common Stock for the five trading days
ending on the day prior to the Redemption Date. The Company shall make the

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                                      -3-

Make-Whole Payment on all Notes called for Provisional Redemption, including
those Notes converted into Common Stock between the Notice Date and the
Provisional Redemption Date.

          Except as set forth above, the Notes are subject to redemption, at any
time on or after November 3, 2004, on at least 20 days and no more than 60 days
notice, in whole or in part, at the election of the Company. The Redemption
Prices (expressed as percentages of the principal amount) are as follows for
Notes redeemed during the periods set forth below:

<Table>
<Caption>
       PERIOD                                                        PERCENTAGE
       <S>                                                           <C>
       Beginning November 3, 2004 through October 31, 2005...........103.143%
       Beginning November 1, 2005 through October 31, 2006...........102.357%
       Beginning November 1, 2006 through October 31, 2007...........101.571%
       Beginning November 1, 2007 and thereafter.....................100.786%
</Table>

in each case together with accrued interest up to but not including the
Redemption Date; provided that if the redemption date is an interest payment
date, interest will be payable to the Holders in whose names the Notes are
registered at the close of business on the relevant record dates.

6         NOTICE OF REDEMPTION

          Notice of redemption will be mailed by first-class mail at least 20
days but not more than 60 days before the Redemption Date to each Holder of
Notes to be redeemed at its registered address. Notes in denominations larger
than $1,000 may be redeemed in part, but only in whole multiples of $1,000. On
and after the Redemption Date, subject to the deposit with the Paying Agent of
funds sufficient to pay the Redemption Price plus accrued interest, if any,
accrued to, but not including, the Redemption Date, interest shall cease to
accrue on Notes or portions of them called for redemption.

7         PURCHASE OF NOTES AT OPTION OF HOLDER UPON A REPURCHASE EVENT

          At the option of the Holder and subject to the terms and conditions of
the Indenture, the Company shall become obligated to purchase all or any part
specified by the Holder (so long as the principal amount of such part is $1,000
or an integral multiple of $1,000 in excess thereof) of the Notes held by such
Holder on the date that is 30 Business Days after the occurrence of a Repurchase
Event, at a purchase price equal to 100% of the principal amount thereof
together with accrued interest up to, but excluding, the Repurchase Event
Payment Date. The Holder shall have the right to withdraw any Repurchase Event
Payment Notice (in whole or in a portion thereof that is $1,000 or an integral
multiple of $1,000 in excess thereof) at any time prior to the close of business
on the Business Day next preceding the Repurchase Event Purchase Date by
delivering a written notice of withdrawal to the Paying Agent in accordance with
the terms of the Indenture.

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                                      -4-

8         CONVERSION

          A Holder of a Note may convert the principal amount of such Note (or
any portion thereof equal to $1,000 or any integral multiple of $1,000 in excess
thereof) into shares of Common Stock at any time prior to the close of business
on November 1, 2008; provided, however, that if the Note is called for
redemption or subject to purchase upon a Repurchase Event, the conversion right
will terminate at the close of business on the Business Day immediately
preceding the redemption date or the Repurchase Event Payment Date, as the case
may be, for such Note or such earlier date as the Holder presents such Note for
redemption or purchase (unless the Company shall default in making the
redemption payment or paying the Repurchase Event payment price, as the case may
be, when due, in which case the conversion right shall terminate at the close of
business on the date such default is cured and such Note is redeemed or
purchased).

          The initial Conversion Price is $47.20 per share, subject to
adjustment under certain circumstances. The number of shares of Common Stock
issuable upon conversion of a Note is determined by dividing the principal
amount of the Note or portion thereof converted by the Conversion Price in
effect on the Conversion Date. No fractional shares will be issued upon
conversion; in lieu thereof, an amount will be paid in cash based upon the
closing price (as defined in the Indenture) of the Common Stock on the trading
day immediately prior to the Conversion Date.

          To convert a Note, a Holder must (a) complete and manually sign the
conversion notice set forth below and deliver such notice to a Conversion Agent,
(b) surrender the Note to a Conversion Agent, (c) furnish appropriate
endorsements and transfer documents if required by a Registrar or a Conversion
Agent, and (d) pay any transfer or similar tax, if required. Notes so
surrendered for conversion (in whole or in part) during the period from the
close of business on any regular record date to the opening of business on the
next succeeding interest payment date (excluding Notes or portions thereof
called for redemption or subject to purchase upon a Repurchase Event on a
redemption date or Repurchase Event Payment Date, as the case may be, during the
period beginning at the close of business on a regular record date and ending at
the opening of business on the first Business Day after the next succeeding
interest payment date, or if such interest payment date is not a Business Day,
the second such Business Day) shall also be accompanied by payment in funds
acceptable to the Company of an amount equal to the interest payable on such
interest payment date on the principal amount of such Note then being converted,
and such interest shall be payable to such registered Holder notwithstanding the
conversion of such Note, subject to the provisions of this Indenture relating to
the payment of defaulted interest by the Company. If the Company defaults in the
payment of interest payable on such interest payment date, the Company shall
promptly repay such funds to such Holder. A Holder may convert a portion of a
Note equal to $1,000 or any integral multiple thereof.

          A Note in respect of which a Holder had delivered a Repurchase Event
Payment Notice exercising the option of such Holder to require the Company to
purchase such

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                                      -5-

Note may be converted only if the Repurchase Event Payment Notice is withdrawn
in accordance with the terms of the Indenture.

9         SUBORDINATION

          The indebtedness evidenced by the Notes is, to the extent and in the
manner provided in the Indenture, subordinate and junior in right of payment to
the prior payment in full in cash of all Senior Indebtedness. Any Holder by
accepting this Note agrees to and shall be bound by such subordination
provisions and authorizes the Trustee to give them effect. In addition to all
other rights of Senior Indebtedness described in the Indenture, the Senior
Indebtedness shall continue to be Senior Indebtedness and entitled to the
benefits of the subordination provisions irrespective of any amendment,
modification or waiver of any terms of any instrument relating to the Senior
Indebtedness or any extension or renewal of the Senior Indebtedness.

10        DENOMINATIONS, TRANSFER, EXCHANGE

          The Notes are in registered form without coupons in denominations of
$1,000 and integral multiples of $1,000. A Holder may register the transfer of
or exchange Notes in accordance with the Indenture. The Registrar may require a
Holder, among other things, to furnish appropriate endorsements and transfer
documents and to pay any taxes or other governmental charges that may be imposed
in relation thereto by law or permitted by the Indenture.

11        PERSONS DEEMED OWNERS

          The Holder of a Note may be treated as the owner of it for all
purposes.

12        UNCLAIMED MONEY

          If money for the payment of principal or interest remains unclaimed
for two years, the Trustee or Paying Agent will pay the money back to the
Company at its written request. After that, Holders entitled to money must look
to the Company for payment.

13        AMENDMENT, SUPPLEMENT AND WAIVER

          Subject to certain exceptions, the Indenture or the Notes may be
amended or supplemented with the consent of the Holders of a majority in
principal amount of the Notes then outstanding, and an existing default or Event
of Default and its consequence or compliance with any provision of the Indenture
or the Notes may be waived in a particular instance with the consent of the
Holders of a majority in principal amount of the Notes then outstanding. Without
the consent of or notice to any Holder, the Company and the Trustee may amend or
supplement the Indenture or the Notes to, among other things, cure any
ambiguity, defect or inconsistency or make any other change that does not
adversely affect the rights of any Holder.

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                                      -6-

14        SUCCESSOR CORPORATION

          When a successor corporation assumes all the obligations of its
predecessor under the Notes and the Indenture in accordance with the terms and
conditions of the Indenture, the predecessor corporation will (except in certain
circumstances specified in the Indenture) be released from those obligations.

15        DEFAULTS AND REMEDIES

          Under the Indenture, an Event of Default includes, in summary: (i)
default for 30 days in payment of any interest on any Notes; (ii) default in
payment of any principal (including, without limitation, any premium, if any) on
the Notes when due; (iii) failure by the Company to observe or perform any
covenant, representation, warranty or other agreement in the Indenture or the
Notes for 45 days after notice to the Company by the Trustee or the holders of
not less than 25% in aggregate principal amount of the Notes then outstanding
voting as a single class; (iv) failure by the Company to comply in any material
respect with any of the provisions of Section 6.09 of the Indenture; (v) failure
by the Company to make any payment at maturity, including any applicable grace
period, in respect of Indebtedness, in an amount in excess of $10,000,000, which
failure shall have continued for thirty (30) days after written notice thereof
shall have been given to the Company by the Trustee or to the Company and a
Responsible Officer of the Trustee by holders of not less than 25% in aggregate
principal amount of the outstanding Notes, which notice specifies such default
and requires the Company to cause such default to be cured or waived and states
that such notice is a "Notice of Default" under the Indenture; (vi) default by
the Company with respect to any Indebtedness, which default results in the
acceleration of such Indebtedness in an amount in excess of $10,000,000, without
such Indebtedness having been discharged or such acceleration having been cured,
waived, rescinded or annulled for a period of thirty (30) days after written
notice thereof shall have been given to the Company by the Trustee or to the
Company and a Responsible Officer of the Trustee by holders of not less than 25%
in aggregate principal amount of the outstanding Notes, which notice requires
the Company to cause such Indebtedness to be discharged or to cause such default
to be cured or waived or such acceleration to be rescinded or annulled and
states that such notice is a "Notice of Default" under the Indenture; and (vii)
certain events of bankruptcy, insolvency or reorganization of the Company. If an
Event of Default (other than as a result of certain events of bankruptcy,
insolvency or reorganization of the Company) occurs and is continuing, the
Trustee or the Holders of at least 25% in principal amount of the Notes then
outstanding may declare all unpaid principal to the date of acceleration on the
Notes then outstanding to be due and payable immediately, all as and to the
extent provided in the Indenture. If an Event of Default occurs as a result of
certain events of bankruptcy, insolvency or reorganization of the Company,
unpaid principal of the Notes then outstanding shall become due and payable
immediately without any declaration or other act on the part of the Trustee or
any Holder, all as and to the extent provided in the Indenture. Holders may not
enforce the Indenture or the Notes except as provided in the Indenture. The
Trustee may require indemnity satisfactory to it before it enforces the
Indenture or the Notes. Subject to certain limitations, Holders of a majority in
principal amount of the Notes then

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                                      -7-

outstanding may direct the Trustee in its exercise of any trust or power. The
Trustee may withhold from Holders notice of any continuing default (except a
default in payment of principal or interest) if it determines that withholding
notice is in their interests. The Company is required to file periodic reports
with the Trustee as to the absence of default.

16        TRUSTEE DEALINGS WITH THE COMPANY

          The Bank of New York, the Trustee under the Indenture, in its
individual or any other capacity, may make loans to, accept deposits from and
perform services for the Company or an Affiliate of the Company, and may
otherwise deal with the Company or an Affiliate of the Company, as if it were
not the Trustee.

17        NO RECOURSE AGAINST OTHERS

          A director, officer, employee or shareholder, as such, of the Company
shall not have any liability for any obligations of the Company under the Notes
or the Indenture nor for any claim based on, in respect of or by reason of such
obligations or their creation. The Holder of this Note by accepting this Note
waives and releases all such liability. The waiver and release are part of the
consideration for the issuance of this Note.

18        AUTHENTICATION

          This Note shall not be valid until the Trustee or an authenticating
agent manually signs the certificate of authentication below on this Note.

19        ABBREVIATIONS AND DEFINITIONS

          Customary abbreviations may be used in the name of the Holder or an
assignee, such as: TEN COM (tenants in common), TEN ENT (tenants by the
entireties), JT TEN (joint tenants with right of survivorship and not as tenants
in common), CUST (Custodian) and UGMA (Uniform Gifts to Minors Act).

          All terms defined in the Indenture and used in this Note but not
specifically defined herein are defined in the Indenture and are used herein as
so defined.

20        INDENTURE TO CONTROL; GOVERNING LAW

          In the case of any conflict between the provisions of this Note and
the Indenture, the provisions of the Indenture shall control. This Note shall be
governed by, and construed in accordance with, the laws of the State of New
York, without regard to principles of conflicts of law.

          The Company will furnish to any Holder, upon written request and
without charge, a copy of the Indenture. Requests may be made to: Cubist
Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421,
Attention: Chief Financial Officer.

<Page>

                                 ASSIGNMENT FORM

To assign this Note, fill in the form below:

I or we assign and transfer this Note to

________________________________________________________________________________
                  (Insert assignee's soc. sec. or tax I.D. no.)

________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________
              (Print or type assignee's name, address and zip code)

and irrevocably appoint

________________________________________________________________________________

agent to transfer this Note on the books of the Company. The agent may
substitute another to act for him or her.

                                                      Your Signature:

Date:
      ------------                                    -------------------------
                                                      (Sign exactly as your name
                                                      appears on the Note)

*Signature guaranteed by:

By:
    ------------------------------------

*   The signature must be guaranteed by an institution which is a member of one
of the following recognized signature guaranty programs: (i) the Securities
Transfer Agent Medallion Program (STAMP); (ii) the New York Stock Exchange
Medallion Program (MSP); (iii) the Stock Exchange Medallion Program (SEMP); or
(iv) such other guaranty program acceptable to the Trustee.

<Page>

                                CONVERSION NOTICE

To convert this Note into Common Stock of the Company, check the box: / /

To convert only part of this Note, state the principal amount to be converted
(must be $1,000 or a multiple of $1,000): $____________.

If you want the stock certificate made out in another person's name, fill in the
form below:

________________________________________________________________________________
                  (Insert assignee's soc. sec. or tax I.D. no.)

________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________
              (Print or type assignee's name, address and zip code)

                                                      Your Signature:

Date:
      ------------                                    -------------------------
                                                      (Sign exactly as your name
                                                      appears on the Note)

*Signature guaranteed by:

By:
    ------------------------------------

*   The signature must be guaranteed by an institution which is a member of one
of the following recognized signature guaranty programs: (i) the Securities
Transfer Agent Medallion Program (STAMP); (ii) the New York Stock Exchange
Medallion Program (MSP); (iii) the Stock Exchange Medallion Program (SEMP); or
(iv) such other guaranty program acceptable to the Trustee.

<Page>

               OPTION TO ELECT REPURCHASE UPON A REPURCHASE EVENT

To:       Cubist Pharmaceuticals, Inc.

          The undersigned registered owner of this Note hereby irrevocably
acknowledges receipt of a notice from Cubist Pharmaceuticals, Inc. (the
"Company") as to the occurrence of a Repurchase Event with respect to the
Company and requests and instructs the Company to redeem the entire principal
amount of this Note, or the portion thereof (which is $1,000 or an integral
multiple thereof) below designated, in accordance with the terms of the
Indenture referred to in this Note at the Repurchase Event payment price,
together with accrued interest to, but excluding, such date.

Dated:
       -----------                                -----------------------------

                                                  -----------------------------

                                                  Signature(s)

                                                  Signature(s)must be guaranteed
                                                  by a guarantor institution
                                                  with membership in an approved
                                                  signature guarantee pursuant
                                                  to Rule 17Ad-15 under the
                                                  Securities Exchange Act of
                                                  1934.

                                                  -----------------------------
                                                  Signature Guaranty

Principal amount to be redeemed
(in an integral multiple of $1,000, if less
than all):

-------------------------------------------
NOTICE: The signature to the foregoing Election must correspond to the Name as
written upon the face of this Note in every particular, without alteration or
any change whatsoever.

<Page>

                         SCHEDULE OF EXCHANGES OF NOTES

          The following exchanges, redemptions, repurchases or conversions of a
part of this global Note have been made:

<Table>
<Caption>
   PRINCIPAL AMOUNT OF THIS
  GLOBAL NOTE FOLLOWING SUCH                             AMOUNT OF DECREASE IN   AMOUNT OF INCREASE IN
DECREASE DATE OF EXCHANGE (OR     AUTHORIZED SIGNATORY    PRINCIPAL AMOUNT OF     PRINCIPAL AMOUNT OF
          INCREASE)                   OF CUSTODIAN          THIS GLOBAL NOTE        THIS GLOBAL NOTE
-----------------------------     --------------------   --------------------    ---------------------
<S>                               <C>                    <C>                     <C>
</Table>

<Page>

            CERTIFICATE TO BE DELIVERED UPON EXCHANGE OR REGISTRATION
                  OF TRANSFER OF TRANSFER RESTRICTED SECURITIES

Re:       5 1/2% Convertible Subordinated Notes due 2008 (the "Notes") of Cubist
          Pharmaceuticals, Inc.

          This certificate  relates to $_______  principal amount of Notes owned
          in (check applicable box)

          / / book-entry or       / / definitive form by _______________________
          (the "Transferor").

          The Transferor has requested a Registrar or the Trustee to exchange or
          register the transfer of such Notes.

          In connection with such request and in respect of each such Note, the
Transferor does hereby certify that the Transferor is familiar with transfer
restrictions relating to the Notes as provided in Section 2.12 of the Indenture
dated as of October 26, 2001 between Cubist Pharmaceuticals, Inc. and The Bank
of New York (the "Indenture"), and the transfer of such Note is being made
pursuant to an effective registration statement under the Securities Act of
1933, as amended (the "Securities Act") (check applicable box) or the transfer
or exchange, as the case may be, of such Note does not require registration
under the Securities Act because (check applicable box):

/ /       Such Note is being transferred pursuant to an effective registration
          statement under the Securities Act.

/ /       Such Note is being acquired for the Transferor's own account, without
          transfer.

/ /       Such Note is being transferred to the Company or a Subsidiary (as
          defined in the Indenture) of the Company.

/ /       Such Note is being transferred to a person the Transferor reasonably
          believes is a "qualified institutional buyer" (as defined in Rule 144A
          or any successor provision thereto ("Rule 144A") under the Securities
          Act) that is purchasing for its own account or for the account of a
          "qualified institutional buyer", in each case to whom notice has been
          given that the transfer is being made in reliance on such Rule 144A,
          and in each case in reliance on Rule 144A.

/ /       Such Note is being transferred pursuant to and in accordance with Rule
          903 or Rule 904 under the Securities Act and, accordingly, the
          Transferor hereby further certifies that (i) the transfer is not being
          made to a person in the United States and (x) at the time the buy
          order was originated, the transferee was outside the United States or
          such Transferor and any Person acting on its behalf reasonably
          believed and believes that the transferee was outside the United
          States or (y) the transaction was executed in, on or through the
          facilities of a designated offshore securities market and neither such
          Transferor nor any Person acting on its behalf knows that the
          transaction was prearranged with a buyer in the United States, (ii) no
          directed selling efforts have been made in contravention of the
          requirements of Rule 903(b) or Rule 904(b) of Regulation S under the
          Securities Act and (iii) the transaction is not part of a plan or
          scheme to evade the registration requirements of the Securities Act
          and (iv) if the proposed transfer is being made prior to the
          expiration of the Restricted Period, the transfer is not being made to
          a U.S. Person or for the account or benefit of a U.S. Person (other
          than an Initial Purchaser).

/ /       Such Note is being transferred pursuant to and in compliance with an
          exemption from the registration requirements under the Securities Act
          in accordance with Rule 144 (or any successor thereto) ("Rule 144")
          under the Securities Act.

/ /       Such Note is being transferred pursuant to and in compliance with an
          exemption from the registration requirements of the Securities Act
          (other than an exemption referred to above) and as a result of which
          such Note will, upon such transfer, cease to be a "restricted
          security" within the

<Page>

                                      -2-

          meaning of Rule 144 under the Securities Act.

          The Transferor acknowledges and agrees that, if the transferee will
hold any such Notes in the form of beneficial interests in a global Note which
is a "restricted security" within the meaning of Rule 144 under the Securities
Act, then such transfer can only be made pursuant to Rule 144A under the
Securities Act and such transferee must be a "qualified institutional buyer"
(as defined in Rule 144A).

Date:
      -------------                     ----------------------------------------
                                               (Insert Name of Transferor)<Page>

                                                                    EXHIBIT 10.4
                                                                  EXECUTION COPY

                          REGISTRATION RIGHTS AGREEMENT

                                                                October 26, 2001

ROBERTSON STEPHENS, INC.
BANC OF AMERICA SECURITIES LLC
J.P. MORGAN SECURITIES INC.
PACIFIC GROWTH EQUITIES, INC.
UBS WARBURG LLC
555 California Street, Suite 2600
San Francisco, California  94104

Ladies and Gentlemen:

          Cubist Pharmaceuticals, Inc., a Delaware corporation (the "Company"),
proposes to issue and sell to Robertson Stephens, Inc., Banc of America
Securities LLC, J.P. Morgan Securities Inc., Pacific Growth Equities, Inc. and
UBS Warburg LLC (collectively, the "Initial Purchasers"), upon the terms set
forth in a purchase agreement of even date herewith (the "Purchase Agreement"),
$125,000,000 aggregate principal amount (plus up to an additional $50,000,000
principal amount) of its 5 1/2% Convertible Subordinated Notes Due 2008 (the
"Initial Securities"). The Initial Securities will be convertible into shares of
common stock, par value $0.001 per share, of the Company (the "Common Stock") at
the conversion price set forth in the Offering Circular dated October 23, 2001.
The Initial Securities are being issued pursuant to an Indenture, dated as of
October 26, 2001 (the "Indenture"), between the Company and The Bank of New
York, as trustee (the "Trustee"). As an inducement to the Initial Purchasers to
enter into the Purchase Agreement, the Company agrees with the Initial
Purchasers, for the benefit of (i) the Initial Purchasers and (ii) the holders
of the Initial Securities and the Common Stock issuable upon conversion of the
Initial Securities (collectively, the "Securities") from time to time until the
expiration of the Shelf Registration Period (as defined in Section 1 below)
(each of the foregoing a "Holder" and collectively the "Holders"), as follows:

          1.   SHELF REGISTRATION. (a) The Company shall, at its cost, prepare
and, within 60 days following the date of the First Closing (as defined in the
Purchase Agreement), file with the Securities and Exchange Commission (the
"Commission") and thereafter use commercially reasonable efforts to cause to be
declared effective as soon as practicable a registration statement on Form S-3
(the "Shelf Registration Statement") relating to the offer and sale of the
Transfer Restricted Securities (as defined in Section 5 below) by the Holders
thereof from time to time in accordance with the methods of distribution set
forth in the Shelf Registration Statement and Rule 415 under the Securities Act
of 1933, as amended (the "Securities Act") (hereinafter, the "Shelf
Registration"); PROVIDED, HOWEVER, that no Holder (other than the Initial
Purchasers) shall be entitled to have the Securities held by it covered by the
Shelf Registration Statement and the Company shall have no obligation to such
Holder under this Agreement unless such Holder agrees in writing to be bound by
all the provisions of this Agreement applicable to Holders.

          (b)  The Company shall use commercially reasonable efforts to keep the
Shelf Registration Statement continuously effective in order to permit the
prospectus included therein (the "Prospectus") to be lawfully delivered by the
Holders of the relevant Securities, for a period of two years from the date of
its effectiveness or such shorter period that will terminate when all the
Securities covered by the Shelf Registration Statement (i) have been sold
pursuant thereto or (ii) may be sold pursuant to Rule 144 under the Securities
Act without regard to volume limits (or any successor rule thereof), assuming
for this
<Page>

purpose that the Holders thereof are not affiliates of the Company (in
any such case, such period being called the "Shelf Registration Period"). The
Company shall be deemed not to have used commercially reasonable efforts to keep
the Shelf Registration Statement effective during the requisite period if it
voluntarily takes any action that would result in Holders of Securities covered
thereby not being able to offer and sell such Securities during that period,
unless such action is (i) required by applicable law or (ii) taken by the
Company in good faith and contemplated by Section 2(b)(v) below, and the Company
thereafter complies with the requirements of Section 2(g) below.

          (c)  Notwithstanding any other provisions of this Agreement to the
contrary, the Company shall cause the Shelf Registration Statement and the
Prospectus and any amendment or supplement thereto, as of the effective date of
the Shelf Registration Statement, amendment or supplement, (i) to comply in all
material respects with the applicable requirements of the Securities Act and the
rules and regulations of the Commission and (ii) except for any untrue
statements or omissions caused by information received in writing from the
Initial Purchasers or any Holder, not to contain any untrue statement of a
material fact or omit to state a material fact required to be stated therein or
necessary in order to make the statements therein, in light of the circumstances
under which they were made, not misleading.

          2.   REGISTRATION PROCEDURES. In connection with the Shelf
Registration  contemplated by Section 1 above,  the following  provisions  shall
apply:

         (a)   The Company shall (i) furnish to the Initial Purchasers, prior to
the filing thereof with the Commission, a copy of the Shelf Registration
Statement and each amendment thereof and each supplement, if any, to the
prospectus included therein and, in the event that any Initial Purchaser (with
respect to any portion of an unsold allotment from the original offering) is
participating in the Shelf Registration Statement, shall use commercially
reasonable efforts to reflect in each such document, when so filed with the
Commission, such comments as such Initial Purchaser reasonably may propose; and
(ii) to the extent required by applicable securities laws, include the names of
the Holders who propose to sell Securities pursuant to the Shelf Registration
Statement as selling securityholders.

          (b)  The Company shall give written notice to the Initial Purchasers
and the Holders of the Securities (which notice pursuant to clauses (ii) through
(v) hereof shall be accompanied by an instruction to suspend the use of the
Prospectus until the requisite changes have been made):

                  (i)   when the Shelf Registration Statement or any amendment
          thereto has been filed with the Commission and when the Shelf
          Registration Statement or any post-effective amendment thereto has
          become effective;

                  (ii)  of any request by the Commission for amendments or
          supplements to the Shelf Registration Statement or the prospectus
          included therein or for additional information;

                  (iii) of the issuance by the Commission of any stop order
          suspending the effectiveness of the Shelf Registration Statement or
          the initiation of any proceedings for that purpose;

                  (iv)  of the receipt by the Company or its legal counsel of
          any notification  with respect to the suspension of the  qualification
          of the  Securities for sale in any  jurisdiction  or the initiation or
          threatening of any proceeding for such purpose; and

                  (v)   of the happening of any event (including without
          limitation discussions or negotiations by the Company with respect to
          a material transaction) that requires the Company to make changes in
          the Shelf

                                       2
<Page>

          Registration Statement or the Prospectus in order that the Shelf
          Registration Statement or the Prospectus does not contain an untrue
          statement of a material fact nor omit to state a material fact
          required to be stated therein or necessary to make the statements
          therein (in the case of the Prospectus, in light of the circumstances
          under which they were made) not misleading.

                  (c)   The Company shall make commercially  reasonable efforts
to obtain the withdrawal, at the earliest possible time, of any order suspending
the effectiveness of the Shelf Registration Statement.

                  (d)   The Company  shall  furnish to each  Holder of
Securities  included  within the  coverage  of the Shelf  Registration,  without
charge,  at  least  one  copy  of  the  Shelf  Registration  Statement  and  any
post-effective amendment thereto,  including financial statements and schedules,
and,  if the Holder so  requests in writing,  all  exhibits  thereto  (including
those, if any, incorporated by reference).

                  (e)   The Company shall,  during the Shelf Registration
Period, deliver to each Holder of Securities included within the coverage of the
Shelf Registration,  without charge, as many copies of the Prospectus (including
each preliminary  prospectus)  included in the Shelf Registration  Statement and
any amendment or supplement thereto as such person may reasonably  request.  The
Company consents, subject to the provisions of this Agreement, to the use of the
Prospectus or any amendment or supplement thereto by each of the selling Holders
of the  Securities  in connection  with the offering and sale of the  Securities
covered by the Prospectus,  or any amendment or supplement thereto,  included in
the Shelf Registration Statement.

                  (f)   Prior to any public offering of the Securities pursuant
to  the  Shelf  Registration  Statement,  the  Company  shall  use  commercially
reasonable efforts to register or qualify,  and shall cooperate with the Holders
of the Securities  included therein and their  respective  counsel in connection
with the  registration  or  qualification  of, the Securities for offer and sale
under the  securities  or "blue sky" laws of such states of the United States as
any Holder of the Securities  reasonably  requests in writing and do any and all
other  acts or things  commercially  reasonable  to enable the offer and sale in
such  jurisdictions of the Securities  covered by such  Registration  Statement;
PROVIDED,  HOWEVER,  that the  Company  shall  not be  required  to (i)  qualify
generally to do business in any  jurisdiction  where it is not then so qualified
or (ii) take any action which would subject it to general  service of process or
to taxation in any jurisdiction where it is not then so subject.

                  (g)   Upon the occurrence of any event contemplated by
paragraphs  (ii)  through (iv) of Section 2(b) above during the period for which
the Company is required to maintain an effective Shelf  Registration  Statement,
the  Company  shall  promptly,  and in the  case of any  event  contemplated  by
paragraph (v) of Section 2(b), no later than 90 days  following the happening of
such  event,   prepare  and  file  a  post-effective   amendment  to  the  Shelf
Registration  Statement or an amendment or supplement to the  Prospectus and any
other  required  document  so  that,  as  thereafter  delivered  to  Holders  or
purchasers  of the  Securities,  the  Prospectus  will  not  contain  an  untrue
statement of a material  fact or omit to state any material  fact required to be
stated  therein or necessary  to make the  statements  therein,  in light of the
circumstances  under  which  they were  made,  not  misleading.  If the  Company
notifies the Initial  Purchasers and the Holders in accordance  with  paragraphs
(ii)  through  (v) of Section  2(b) above to suspend  the use of the  Prospectus
until the requisite  changes to the Prospectus  have been made, then the Initial
Purchasers  and the  Holders  shall  suspend  use of such  prospectus  until and
including  the date when the  Initial  Purchasers  and the  Holders  shall  have
received such amended or supplemented  prospectus pursuant to this Section 2(g).
Notwithstanding anything in this Agreement to the contrary, the Company shall be
able to suspend use of the Shelf Registration statement by the Holders or period
of not more than 90 consecutive days or an aggregate of 120 days in any 12-month
period  after  delivery by the Company of the  certificate  referred to above in
Section 2(b)(v). During the such periods, none of the Holders shall

                                       3
<Page>

offer or sell any of the  Securities  pursuant to or in reliance  upon the Shelf
Registration Statement (or the prospectus relating thereto).

                  (h)   Not  later   than  the   effective   date  of  the
Shelf  Registration  Statement,  the Company will provide  CUSIP numbers for the
Initial  Securities  registered  under the  Shelf  Registration  Statement,  and
provide the Trustee with printed  certificates for the Initial Securities,  in a
form eligible for deposit with The Depository Trust Company.

                  (i)   The Company will comply with all rules and regulations
of the  Commission to the extent and so long as they are applicable to the Shelf
Registration  and will make  generally  available  to its  security  holders (or
otherwise  provide in accordance  with Section 11(a) of the  Securities  Act) an
earnings statement  satisfying the provisions of Section 11(a) of the Securities
Act,  no later than 45 days after the end of a 12-month  period (or 90 days,  if
such period is a fiscal year)  beginning  with the first month of the  Company's
first  fiscal  quarter   commencing  after  the  effective  date  of  the  Shelf
Registration Statement, which statement shall cover such 12-month period.

                  (j)   The Company shall cause the Indenture to be qualified
under the Trust Indenture Act of 1939, as amended (the "Trust  Indenture  Act"),
in a timely manner and  containing  such changes,  if any, as shall be necessary
for such  qualification.  In the event that such qualification would require the
appointment  of a new trustee under the  Indenture,  the Company shall appoint a
new trustee thereunder pursuant to the applicable provisions of the Indenture.

                  (k)   The Company may require each Holder of Securities to be
sold pursuant to the Shelf Registration Statement to furnish to the Company such
information  regarding the Holder and the  distribution of the Securities as the
Company  may from time to time  reasonably  require for  inclusion  in the Shelf
Registration  Statement,  and the Company may exclude from such registration the
Securities  of any  Holder  that  fails to  furnish  such  information  within a
reasonable time after receiving such request.

                  (l)   The Company shall enter into such agreements reasonably
satisfactory  to the  Company  and take all such  other  reasonable  actions  in
connection  therewith  (including those reasonably requested by the Holders of a
majority in aggregate principal amount of the Securities being sold) in order to
expedite or facilitate the sale of such  Securities.  The Company shall (i) make
such  representations  and  warranties to the Holders of such  Securities,  with
respect to the  business  of the Company and its  subsidiaries  (including  with
respect to businesses or assets acquired or to be acquired by any of them),  and
the Registration  Statement,  Prospectus and documents,  if any, incorporated or
deemed to be incorporated by reference therein, in each case, in form, substance
and scope as are  customarily  made by issuers to  underwriters  in underwritten
offerings and reasonably  acceptable to the Company, and confirm the same if and
when  requested;  (ii) seek to obtain  opinions  of counsel to the  Company  and
updates thereof (which counsel and opinions (in form, scope and substance) shall
be reasonably  satisfactory to the Holders of a majority in aggregate  principal
amount of the Securities),  and counsel to the Holders (as selected  pursuant to
Section 3(b)), covering the matters customarily covered in opinions requested in
underwritten  offerings  (including  any  such  matters  as  may  be  reasonably
requested by such counsel); (iii) use all reasonable efforts to obtain customary
"cold comfort" letters and updates thereof from the independent certified public
accountants of the Company (and, if necessary,  any other independent  certified
public  accountants of any subsidiary of the Company or of any business acquired
by the Company  for which  financial  statements  and  financial  data is, or is
required  to be,  included  in the  Registration  Statement),  addressed  (where
reasonably possible) to each selling Holder of Securities, such letters to be in
customary  form and covering  matters of the type  customarily  covered in "cold
comfort"  letters in connection with  underwritten  offerings;  and (iv) deliver
such documents and certificates as may be reasonably requested by the Holders of
majority in aggregate principal amount of the Securities being

                                       4
<Page>

sold or their  counsel,  if any,  to  evidence  the  continued  validity  of the
representations and warranties made pursuant to clause (i) of this Section 2(l).

                  (m)   The Company shall (i) make reasonably available for
inspection by the Holders,  any  underwriter  participating  in any  disposition
pursuant to the Shelf  Registration  Statement and any  attorney,  accountant or
other  agent  retained  by the  Holders or any such  underwriter,  all  relevant
financial and other records, pertinent corporate documents and properties of the
Company and (ii) cause the Company's officers, directors, employees, accountants
and  auditors to supply all  relevant  information  reasonably  requested by the
Holders or any such  underwriter,  attorney,  accountant  or agent in connection
with the Shelf  Registration  Statement,  in each case,  as shall be  reasonably
necessary to enable such persons, to conduct a reasonable  investigation  within
the meaning of Section 11 of the Securities  Act;  PROVIDED,  HOWEVER,  that the
foregoing  inspection  and  information  gathering  shall be coordinated on your
behalf by you and on behalf of the other parties,  by one counsel  designated by
and on behalf of such other parties as described in Section 3 below.

                  (n)   The Company will use commercially reasonable efforts to
(a) if the Initial  Securities have been rated prior to the initial sale of such
Initial Securities, confirm such ratings will apply to the Securities covered by
a Registration  Statement,  or (b) if the Initial Securities were not previously
rated, cause the Securities covered by a Registration Statement to be rated with
the  appropriate  rating  agencies,  if so requested by holders of a majority in
aggregate  principal  amount of  Securities  covered  by the Shelf  Registration
Statement, or by the managing underwriters, if any.

                  (o)   In the event that any broker-dealer registered under the
Exchange Act shall  participate as a member of a selling group or "assist in the
distribution"  (within  the meaning of the  Conduct  Rules (the  "Rules") of the
National Association of Securities Dealers, Inc. ("NASD")) thereof, whether as a
Holder of such Securities or as a placement or sales agent or a broker or dealer
in respect thereof, or otherwise,  the Company will assist such broker-dealer in
complying with the requirements of such Rules, including, without limitation, by
(i) if such Rules, including Rule 2720, shall so require,  engaging a "qualified
independent  underwriter"  (as  defined  in Rule  2720)  to  participate  in the
preparation of the Shelf Registration Statement relating to such Securities,  to
exercise usual standards of due diligence in respect thereto and, if any portion
of the offering  contemplated by such  Registration  Statement is made through a
placement  or sales  agent,  to  recommend  the yield of such  Securities,  (ii)
indemnifying any such "qualified  independent  underwriter" to the extent of the
indemnification of underwriters  provided in Section 5 below and (iii) providing
such  information  to such  broker-dealer  as may be  required in order for such
broker-dealer to comply with the requirements of the Rules.

                  (p)   The Company shall use commercially reasonable efforts to
take all other steps  necessary  to effect the  registration  of the  Securities
covered by a Registration Statement contemplated hereby.

          3.   REGISTRATION EXPENSES.  (a) All expenses,  other than
underwriting, brokerage and other selling commissions and discounts, incident to
the Company's performance of and compliance with this Agreement will be borne by
the Company,  regardless  of whether a  Registration  Statement is ever filed or
becomes effective, including without limitation:

                  (i)   all registration and filing fees and expenses;

                  (ii)  all  fees  and  expenses  of  compliance   with  federal
          securities and state "blue sky" or securities laws;

                                       5
<Page>

                  (iii) all   expenses   of   printing   (including   printing
          certificates   for  the  Securities  to  be  issued  and  printing  of
          Prospectuses), messenger and delivery services and telephone;

                  (iv)  all fees and disbursements of counsel for the Company;

                  (v) all application and filing fees in connection with listing
          the  Securities  on  a  national   securities  exchange  or  automated
          quotation system pursuant to the requirements hereof; and

                  (vi) all  fees  and  disbursements  of  independent  certified
          public  accountants  of the  Company  (including  the  expenses of any
          special  audit and  comfort  letters  required  by or incident to such
          performance).

The Company will bear its internal expenses (including, without limitation, all
salaries and expenses of its officers and employees performing legal or
accounting duties), the expenses of any annual audit and the fees and expenses
of any person, including special experts, retained by the Company.

          (b)  In connection with the Shelf Registration Statement required by
this Agreement, the Company will reimburse the Initial Purchasers and the
Holders of Securities covered by the Shelf Registration Statement up to a
maximum of $10,000 for the reasonable fees and disbursements of not more than
one counsel, which shall be the firm acting as counsel for the Initial
Purchasers in connection herewith unless a different firm is designated by the
Holders of a majority in principal amount of the Securities covered by the Shelf
Registration Statement (provided that Holders of Common Stock issued upon the
conversion of the Initial Securities shall be deemed to be Holders of the
aggregate principal amount of Initial Securities from which such Common Stock
was converted) to act as counsel for the Holders in connection therewith.

          4.   INDEMNIFICATION. (a) The Company agrees to indemnify and hold
harmless each Holder and each person, if any, who controls such Holder within
the meaning of the Securities Act or the Exchange Act (each Holder, and such
controlling persons are referred to collectively as the "Indemnified Parties")
from and against any losses, claims, damages or liabilities, joint or several,
or any actions in respect thereof (including, but not limited to, any losses,
claims, damages, liabilities or actions relating to purchases and sales of the
Securities) to which each Indemnified Party may become subject under the
Securities Act, the Exchange Act or otherwise, insofar as such losses, claims,
damages, liabilities or actions arise out of or are based upon any untrue
statement or alleged untrue statement of a material fact contained in the Shelf
Registration Statement or prospectus including any document incorporated by
reference therein, or in any amendment or supplement thereto or in any
preliminary prospectus relating to the Shelf Registration, or arise out of, or
are based upon, the omission or alleged omission to state therein a material
fact required to be stated therein or necessary to make the statements therein
not misleading, and shall reimburse, as incurred, the Indemnified Parties for
any legal or other expenses reasonably incurred by them in connection with
investigating or defending any such loss, claim, damage, liability or action in
respect thereof; PROVIDED, HOWEVER, that (i) the Company shall not be liable in
any such case to the extent that such loss, claim, damage or liability arises
out of or is based upon any untrue statement or alleged untrue statement or
omission or alleged omission made in the Shelf Registration Statement or
prospectus or in any amendment or supplement thereto or in any preliminary
prospectus relating to the Shelf Registration in reliance upon and in conformity
with written information pertaining to such Holder and furnished to the Company
by or on behalf of such Holder specifically for inclusion therein and (ii) with
respect to any untrue statement or omission or alleged untrue statement or
omission made in any preliminary prospectus relating to the Shelf Registration
Statement, the indemnity agreement contained in this subsection (a) shall not
inure to the benefit of any Holder from whom the person asserting any such
losses, claims, damages or liabilities purchased the Securities concerned, to
the extent that a

                                       6
<Page>

prospectus relating to such Securities was required to be delivered by such
Holder under the Securities Act in connection with such purchase and any such
loss, claim, damage or liability of such Holder results from the fact that there
was not sent or given to such person, at or prior to the written confirmation of
the sale of such Securities to such person, a copy of the final prospectus if
the Company had previously furnished copies thereof to such Holder; PROVIDED
FURTHER, HOWEVER, that this indemnity agreement will be in addition to any
liability which the Company may otherwise have to such Indemnified Party. The
Company shall also indemnify underwriters, their officers and directors and each
person who controls such underwriters within the meaning of the Securities Act
or the Exchange Act to the same extent as provided above with respect to the
indemnification of the Holders of the Securities if requested by such Holders.

          (b)  Each Holder, severally and not jointly, will indemnify and hold
harmless the Company, its officers and directors and each person, if any, who
controls the Company within the meaning of the Securities Act or the Exchange
Act from and against any losses, claims, damages or liabilities or any actions
in respect thereof, to which the Company or any such controlling person may
become subject under the Securities Act, the Exchange Act or otherwise, insofar
as such losses, claims, damages, liabilities or actions arise out of or are
based upon any untrue statement or alleged untrue statement of a material fact
contained in the Shelf Registration Statement or prospectus or in any amendment
or supplement thereto or in any preliminary prospectus relating to the Shelf
Registration, or arise out of or are based upon the omission or alleged omission
to state therein a material fact necessary to make the statements therein not
misleading, but in each case only to the extent that the untrue statement or
omission or alleged untrue statement or omission was made in reliance upon and
in conformity with written information pertaining to such Holder and furnished
to the Company by or on behalf of such Holder specifically for inclusion
therein; and, subject to the limitation set forth immediately preceding this
clause, shall reimburse, as incurred, the Company for any legal or other
expenses reasonably incurred by the Company or any such controlling person in
connection with investigating or defending any loss, claim, damage, liability or
action in respect thereof. This indemnity agreement will be in addition to any
liability which such Holder may otherwise have to the Company or any of its
controlling persons.

          (c)  Promptly after receipt by an indemnified party under this Section
4 of notice of the commencement of any action or proceeding (including a
governmental investigation), such indemnified party will, if a claim in respect
thereof is to be made against the indemnifying party under this Section 4,
notify the indemnifying party of the commencement thereof; but the omission so
to notify the indemnifying party will not, in any event, relieve the
indemnifying party from any obligations to any indemnified party other than the
indemnification obligation provided in paragraph (a) or (b) above. In case any
such action is brought against any indemnified party, and it notifies the
indemnifying party of the commencement thereof, the indemnifying party will be
entitled to participate therein and, to the extent that it may wish, jointly
with any other indemnifying party similarly notified, to assume the defense
thereof, with counsel reasonably satisfactory to such indemnified party (who
shall not, except with the consent of the indemnified party, be counsel to the
indemnifying party), and after notice from the indemnifying party to such
indemnified party of its election so to assume the defense thereof the
indemnifying party will not be liable to such indemnified party under this
Section 4 for any legal or other expenses, other than reasonable costs of
investigation, subsequently incurred by such indemnified party in connection
with the defense thereof. No indemnifying party shall, without the prior written
consent of the indemnified party, effect any settlement of any pending or
threatened action in respect of which any indemnified party is or could have
been a party and indemnity could have been sought hereunder by such indemnified
party unless such settlement (i) includes an unconditional release of such
indemnified party from all liability on any claims that are the subject matter
of such action, and (ii) does not include

                                       7
<Page>

a statement as to or an admission of fault, culpability or a failure to act by
or on behalf of any indemnified party.

          (d)  If the indemnification provided for in this Section 4 is
unavailable or insufficient to hold harmless an indemnified party under
subsections (a) or (b) above, then each indemnifying party shall contribute to
the amount paid or payable by such indemnified party as a result of the losses,
claims, damages or liabilities (or actions in respect thereof) referred to in
subsection (a) or (b) above in such proportion as is appropriate to reflect the
relative fault of the indemnifying party or parties on the one hand and the
indemnified party on the other in connection with the statements or omissions
that resulted in such losses, claims, damages or liabilities (or actions in
respect thereof) as well as any other relevant equitable considerations. The
relative fault of the parties shall be determined by reference to, among other
things, whether the untrue or alleged untrue statement of a material fact or the
omission or alleged omission to state a material fact relates to information
supplied by the Company on the one hand or such Holder or such other indemnified
party, as the case may be, on the other, and the parties' relative intent,
knowledge, access to information and opportunity to correct or prevent such
statement or omission. The amount paid by an indemnified party as a result of
the losses, claims, damages or liabilities referred to in the first sentence of
this subsection (d) shall be deemed to include any legal or other expenses
reasonably incurred by such indemnified party in connection with investigating
or defending any action or claim which is the subject of this subsection (d).
Notwithstanding any other provision of this Section 4(d), the Holders shall not
be required to contribute any amount in excess of the amount by which the net
proceeds received by such Holders from the sale of the Securities pursuant to
the Shelf Registration Statement exceeds the amount of damages which such
Holders have otherwise been required to pay by reason of such untrue or alleged
untrue statement or omission or alleged omission. No person guilty of fraudulent
misrepresentation (within the meaning of Section 11(f) of the Securities Act)
shall be entitled to contribution from any person who was not guilty of such
fraudulent misrepresentation. For purposes of this paragraph (d), each person,
if any, who controls such indemnified party within the meaning of the Securities
Act or the Exchange Act shall have the same rights to contribution as such
indemnified party and each person, if any, who controls the Company within the
meaning of the Securities Act or the Exchange Act shall have the same rights to
contribution as the Company.

          (e)  The agreements contained in this Section 4 shall survive the sale
of the Securities pursuant to the Shelf Registration Statement and shall remain
in full force and effect, regardless of any termination or cancellation of this
Agreement or any investigation made by or on behalf of any indemnified party.

          5.   ADDITIONAL INTEREST UNDER CERTAIN CIRCUMSTANCES. (a) Additional
interest (the "Additional Interest") with respect to the Initial Securities
shall be assessed as follows if any of the following events occurs (each such
event in clauses (i) through (iii) below being herein called a "Registration
Default"):

                  (i)   the Shelf Registration Statement has not been filed with
          the Commission by the ninetieth (90) day after the first date of
          original issuance of the Initial Securities;

                  (ii)  the Shelf Registration Statement has not been declared
          effective by the Commission by the one hundred eightieth (180) day
          after the first date of original issue of the Initial Securities; or

                  (iii) the Shelf Registration Statement is declared effective
          by the Commission but (A) the Shelf Registration Statement thereafter
          ceases to be effective or (B) the Shelf Registration Statement or the
          Prospectus ceases to be usable in connection with resales of Transfer
          Restricted Securities (as defined below) during the periods specified
          herein and (1) the Company shall not have cured the shelf registration
          statement within five (5) business days by filing a post-effective

                                       8
<Page>

          amendment or a report filed pursuant to the Exchange Act or (2) if
          applicable, the suspension period described above shall not have been
          terminated by the ninetieth (90)consecutive day thereof, as the case
          may be;.

          Each of the foregoing will constitute a Registration Default whatever
the reason for any such event and whether it is voluntary or involuntary or is
beyond the control of the Company or pursuant to operation of law or as a result
of any action or inaction by the Commission .

          Additional Interest shall accrue on the Initial Securities over and
above the interest set forth in the title of the Initial Securities from and
including the date on which any such Registration Default shall occur to but
excluding the date on which all such Registration Defaults have been cured, at a
rate of 0.50% per annum (the "Additional Interest Rate").

          (b)  A Registration Default referred to in Section 5(a)(iii) above
shall be deemed not to have occurred and be continuing in relation to the Shelf
Registration Statement or the related prospectus if (i) such Registration
Default has occurred solely as a result of (x) the filing of a post-effective
amendment to the Shelf Registration Statement to incorporate annual audited
financial information with respect to the Company where such post-effective
amendment is not yet effective and needs to be declared effective to permit
Holders to use the related prospectus or (y) other material events, with respect
to the Company that would need to be described in such Shelf Registration
Statement or the related prospectus and (ii) in the case of clause (y), the
Company is proceeding promptly and in good faith to amend or supplement the
Shelf Registration Statement and related prospectus to describe such events as
required by paragraph 2(h) hereof; provided, however, that in any case if such
Registration Default occurs for a continuous period in excess of 90 consecutive
days or an aggregate of 120 days in any 12 month period, Additional Interest
shall be payable in accordance with the above paragraph from the day such
Registration Default occurs until such Registration Default is cured.

          (c)  Any amounts of Additional Interest due pursuant to Section 5(a)
above will be payable in cash on the regular interest payment dates with respect
to the Initial Securities. The amount of Additional Interest will be determined
by multiplying the applicable Additional Interest Rate by the principal amount
of the Initial Securities, further multiplied by a fraction, the numerator of
which is the number of days such Additional Interest Rate was applicable during
such period (determined on the basis of a 360-day year comprised of twelve
30-day months), and the denominator of which is 360.

          (d)  "Transfer Restricted Securities" means each Security until (i)
the date on which  such  Security  has been  effectively  registered  under  the
Securities  Act and  disposed  of in  accordance  with  the  Shelf  Registration
Statement or (ii) the date on which such Security is  distributed  to the public
pursuant to Rule 144 under the  Securities  Act or is saleable  pursuant to Rule
144 under the  Securities  Act without regard to volume limits (or any successor
rule thereof),.

          6.   RULES 144 AND 144A. The Company shall use commercially reasonable
efforts to file the reports required to be filed by it under the Securities Act
and the Exchange Act in a timely manner and, if at any time the Company is not
required to file such reports, it will, upon the request of any Holder, make
publicly available other information so long as necessary to permit sales of
their securities pursuant to Rules 144 and 144A under the Securities Act. The
Company covenants that it will take such further action as any Holder may
reasonably request, all to the extent required from time to time to enable such
Holder to sell Transfer Restricted Securities without registration under the
Securities Act within the limitation of the exemptions provided by Rules 144 and
144A (including the requirements of Rule 144A(d)(4)). The Company will provide a
copy of this Agreement to prospective purchasers of Securities identified to the
Company by the Initial Purchasers upon request. Upon the request of any

                                       9
<Page>

Holder, the Company shall deliver to such Holder a written statement as to
whether it has complied with such requirements. Notwithstanding the foregoing,
nothing in this Section 6 shall be deemed to require the Company to register any
of its securities pursuant to the Exchange Act.

          7.   MISCELLANEOUS.

          (a)  REMEDIES. The Company acknowledges and agrees that any failure by
the Company to comply with its obligations under Section 1 above may result in
material irreparable injury to the Initial Purchasers or the Holders for which
there is no adequate remedy at law, that it will not be possible to measure
damages for such injuries precisely and that, in the event of any such failure,
the Initial Purchasers or any Holder may obtain such relief as may be required
to specifically enforce the Company's obligations under Section 1 above. The
Company further agrees to waive the defense in any action for specific
performance that a remedy at law would be adequate.

          (b)  NO INCONSISTENT AGREEMENTS. The Company will not on or after the
date of this Agreement enter into any agreement with respect to its securities
that is inconsistent with the rights granted to the Holders in this Agreement or
otherwise conflicts with the provisions hereof. The rights granted to the
Holders hereunder do not in any way conflict with and are not inconsistent with
the rights granted to the holders of the Company's securities under any
agreement in effect on the date hereof.

          (c)  AMENDMENTS AND WAIVERS. The provisions of this Agreement may not
be amended, modified or supplemented, and waivers or consents to departures from
the provisions hereof may not be given, except by the Company and the written
consent of the holders of a majority in principal amount of the Securities
affected by such amendment, modification, supplement, waiver or consents
(provided that holders of Common Stock issued upon conversion of Initial
Securities shall not be deemed holders of Common Stock, but shall be deemed to
be holders of the aggregate principal amount of Initial Securities from which
such Common Stock was converted). Without the consent of the Holder of each
Initial Security, however, no modification may change the provisions relating to
the payment of Additional Interest.

          (d)  NOTICES. All notices and other communications provided for or
permitted hereunder shall be made in writing by hand delivery, first-class mail,
facsimile transmission, or air courier which guarantees overnight delivery:

                  (1)   if to a Holder of the Securities, at the most current
          address given by such Holder to the Company.

                                       10
<Page>

                  (2)   if to the Initial Purchasers:

                           Robertson Stephens, Inc.
                           555 California Street
                           San Francisco, California  94104
                           Facsimile:  415.676.2696
                           Attention:  General Counsel

          with a copy to:  Hale and Dorr LLP
                           60 State Street
                           Boston, Massachusetts 02109
                           Fax No.:  (617) 526-5000
                           Attention:  Mark L. Johnson

                  (3)      if to the Company:

                           Cubist Pharmaceuticals, Inc.
                           24 Emily Street
                           Cambridge, Massachusetts 02139
                           Fax No.:  (617) 576-0232
                           Attention:  President and Chief Executive Officer

          with a copy to:  Bingham Dana LLP
                           150 Federal Street
                           Boston, Massachusetts 02110
                           Fax No.:  (617) 951-8736
                           Attention:  Julio E. Vega
                                  Matthew J. Cushing

          All such notices and communications shall be deemed to have been duly
given: at the time delivered by hand, if personally delivered; three business
days after being deposited in the mail, postage prepaid, if mailed; when receipt
is acknowledged by recipient's facsimile machine operator, if sent by facsimile
transmission; and on the day delivered, if sent by overnight air courier
guaranteeing next day delivery.

          (e)  THIRD PARTY BENEFICIARIES. The Holders shall be third party
beneficiaries to the agreements made hereunder between the Company, on the one
hand, and the Initial Purchasers, on the other hand, and shall have the right to
enforce such agreements directly to the extent they may deem such enforcement
necessary or advisable to protect their rights or the rights of Holders
hereunder.

          (f)  SUCCESSORS AND ASSIGNS. This Agreement shall be binding upon the
Company and its successors and assigns.

          (g)  COUNTERPARTS. This Agreement may be executed in any number of
counterparts and by the parties hereto in separate counterparts, each of which
when so executed shall be deemed to be an original and all of which taken
together shall constitute one and the same agreement.

          (h)  HEADINGS. The headings in this Agreement are for convenience of
reference only and shall not limit or otherwise affect the meaning hereof.

                                       11
<Page>

          (i)  GOVERNING Law. THIS AGREEMENT SHALL BE GOVERNED BY, AND CONSTRUED
IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO
PRINCIPLES OF CONFLICTS OF LAWS.

          By the execution and delivery of this Agreement, each of the Company
and the Initial Purchasers submits to the nonexclusive jurisdiction of any
federal or state court in the State of New York.

          (j)  SEVERABILITY. If any one or more of the provisions contained
herein, or the application thereof in any circumstance, is held invalid, illegal
or unenforceable, the validity, legality and enforceability of any such
provision in every other respect and of the remaining provisions contained
herein shall not be affected or impaired thereby.

          (k)  SECURITIES HELD BY THE COMPANY. Whenever the consent or approval
of Holders of a specified percentage of principal amount of Securities is
required hereunder, Securities held by the Company or its affiliates (other than
subsequent Holders of Securities if such subsequent Holders are deemed to be
affiliates solely by reason of their holdings of such Securities) shall not be
counted in determining whether such consent or approval was given by the Holders
of such required percentage.

                [REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

                                       12
<Page>

          If the foregoing is in accordance with your understanding of our
agreement, please sign and return to the Company a counterpart hereof, whereupon
this instrument, along with all counterparts, will become a binding agreement
between the Initial Purchasers and the Company in accordance with its terms.

                                              Very truly yours,

                                              CUBIST PHARMACEUTICALS, INC.

                                              By       /s/ Thomas A. Shea
                                                  ---------------------------
                                                  Vice President, Finance and
                                                  Chief Financial Officer

The foregoing Registration Rights
Agreement is hereby confirmed and
accepted as of the date first above
written.

ROBERTSON STEPHENS, INC.
BANC OF AMERICA SECURITIES LLC
J.P. MORGAN SECURITIES INC.
PACIFIC GROWTH EQUITIES, INC.
UBS WARBURG LLC

By:  Robertson Stephens, Inc.

     By:       /s/ Mitchell Whiteford
         -------------------------------
         Name:  Mitch Whiteford
         Title: Managing Director

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