Exhibit 10.1

VERTEX PHARMACEUTICALS INCORPORATED

EMPLOYEE STOCK PURCHASE PLAN

(as amended and restated

May 31, 2007)

ARTICLE 1

PURPOSE AND DEFINITIONS

 SECTION 1.1.  PURPOSE.  The purpose of the Vertex Pharmaceuticals Incorporated
Employee Stock Purchase Plan is to provide employees with an opportunity to
purchase Common Stock in the Company through payroll deductions, thereby
encouraging employees to share in the economic growth and success of the Company
through stock ownership.

 SECTION 1.2.  DEFINITIONS.  Whenever used in the Plan, unless the context
clearly indicates otherwise, the following terms shall have the following
meanings:

(a)                                “BENEFICIARY” with respect to a Participant,
means the beneficiary designated by the Participant under the group term life
insurance plan maintained by the Company or such other beneficiary as may be
designated by a Participant for purposes of this Plan.

(b)                               “BOARD OF DIRECTORS” means the Board of
Directors of the Company.

(c)                                “CODE” means the Internal Revenue Code of
1986, as the same may be amended from time to time, and references thereto shall
include the valid Treasury regulations issued thereunder.

(d)                               “COMMITTEE” means the Management Development
and Compensation Committee of the Board of Directors or such other committee of
the Board of Directors designated by the  Board of Directors to administer the
Company’s equity compensation plans.

(e)                                “COMMON STOCK” means shares of the $.01 par
value common stock of the Company and any other stock or securities resulting
from the adjustment thereof or substitution therefor as described in
Section 3.4.

(f)                                  “COMPANY” means Vertex Pharmaceuticals
Incorporated or any successor by merger, purchase, or otherwise.

(g)                               “COMPENSATION” means the cash compensation
received by an Employee for services, including pre-tax employee compensation
made to the Company’s 401(k) savings plan, but not including overtime or
bonuses.

(h)                               “EFFECTIVE DATE” means July 1, 1992.

(i)                                   “ELECTION” means an election by a
Participant to terminate an Offering Period on the first Purchase Date of such
Offering Period, which election shall be made within such Offering Period and
prior to such First Purchase Date and shall be in writing on a form furnished by
the Company for such purpose and shall be made by having such Participant
complete, sign and file such form with the Company in the manner prescribed by
the Company.

(j)                                   “EMPLOYEE” means any person who receives a
regular stated compensation from the Company or a Subsidiary other than a
pension, severance pay, retainer, or fee under contract.

(k)                                “FAIR MARKET VALUE” of a Share of Common
Stock on a particular date shall be the average of the highest and lowest quoted
selling prices on such date (the “valuation date”) on the securities market
where the Common Stock of the Company is traded, or if there were no sales on
the valuation date, on the next preceding date within a reasonable period (as
determined in the sole discretion of the Committee) on which there were sales.
In the event that there were no sales in such a market within a reasonable
period, the fair market value shall be as determined in good faith by the
Committee in its sole discretion. The Fair Market Value as determined in this
paragraph shall be rounded down to the next lower whole cent if the foregoing
calculation results in fractional cents.

  

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(l)                                   “OFFERING” means the offering of shares of
Common Stock to Participants pursuant to this Plan.

(m)                             “OFFERING DATE” means each May 15 and
November 15. If any such date shall fall other than on a business day, then the
Offering Date shall be the next succeeding business day.

(n)                               “OFFERING PERIOD” means either (i) the period
from an Offering Date through the second Purchase Date following such Offering
Date or (ii) if a Participant validly exercises an Election, the period from an
Offering Date through the first Purchase Date following such Offering Date.

(o)                               “PARTICIPANT” means an Employee who has
elected to participate in the Plan.

(p)                               “PURCHASE DATE” means each May 14 and
November 14.

(q)                               “PLAN” means the Vertex Pharmaceuticals
Incorporated Employee Stock Purchase Plan, an “employee stock purchase plan”
within the meaning of Section 423(b) of the Code, together with any and all
amendments thereto.

(r)                                  “STOCK PURCHASE ACCOUNT,” with respect to a
Participant, means the account established on the books and records of the
Company or a Subsidiary for such Participant representing the payroll deductions
credited to such account in accordance with the provisions of the Plan.

(s)                                “SUBSIDIARY” means any corporation, fifty
percent (50%) or more of the total combined voting power of all classes of stock
of which is beneficially owned, directly or indirectly, by the Company.

ARTICLE II

PARTICIPATION

 SECTION 2.1.  PARTICIPATION REQUIREMENTS.

(a)                                COMMENCEMENT OF PARTICIPATION.  Subject to
Section 2.2 and Section 3.2(b), each person who becomes an Employee after the
Effective Date may become a Participant in the Plan on any Offering Date
following the date on which such person becomes an Employee.

(b)                               ELIGIBILITY OF FORMER PARTICIPANTS.  If a
person terminates employment with the Company after becoming a Participant and
subsequently resumes employment with the Company, such person will again become
eligible to participate on the Offering Date next following such resumption of
employment with the Company.

 SECTION 2.2.  EXCLUSIONS.  Notwithstanding any provision of the Plan to the
contrary, in no event shall the following persons be eligible to participate in
the Plan:

(a)                                Any Employee whose customary employment is
twenty (20) hours or less per week;

(b)                               Any Employee whose customary employment is for
not more than five (5) months in any calendar year; or

(c)                                Any Employee who, as of the beginning of an
Offering Period, owns (or under Section 423(b)(3) of the Code would be deemed to
own) stock possessing five percent (5%) or more of the total combined voting
power or value of all classes of stock of the Company or a Subsidiary.

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ARTICLE III

OFFERING OF COMMON STOCK

 SECTION 3.1.  RESERVATION OF COMMON STOCK.  The Board of Directors shall
reserve 1,748,660 shares of Common Stock for issuance under the Plan after
March 17, 2004, subject to adjustment in accordance with Section 3.4, provided
that no more than 248,660 of such shares shall be issued prior to May 15, 2004.

 SECTION 3.2.  OFFERING OF COMMON STOCK.

(a)                                GENERAL.  Subject to Section 3.2(b), each
Participant in the Plan on an Offering Date shall be entitled to purchase shares
of Common Stock on each Purchase Date within the Offering Period that begins
with such Offering Date with the amounts deducted from such Participant’s
Compensation during such Offering Period pursuant to Article IV, provided,
however, that a Participant shall not participate in more than one Offering
Period simultaneously. The purchase price for such shares of Common Stock shall
be determined under Section 3.3.

(b)                               LIMITATIONS.  Notwithstanding Section 3.2(a),
no employee may accrue rights to purchase shares of Common Stock attributable to
an Offering Period in excess of $25,000 of fair market value of such shares
(measured as of the relevant Offering Date) for each calendar year during which
such rights are outstanding. For any year, this limit shall be further reduced
by the fair market value of stock (measured as of the relevant Offering Date for
such stock) purchasable under any prior outstanding rights relating to such
calendar year under this Plan and all other Code section 423 employee stock
purchase plans of the Company or any Subsidiary. This paragraph is intended to
be consistent with the limitation of Code section 423(b)(8) and shall be
interpreted accordingly.

 SECTION 3.3.  DETERMINATION OF PURCHASE PRICE FOR OFFERED COMMON STOCK.  The
purchase price per share of the shares of Common Stock to be acquired by a
Participant on a Purchase Date pursuant to an Offering shall be equal to
eighty-five percent (85%) of the lesser of:

(a)                                the Fair Market Value of a share of Common
Stock on the Offering Date for such Offering Period; or

(b)                               the Fair Market Value of a share of Common
Stock on such Purchase Date;

provided, however, in no event shall the purchase price be less than the par
value of a share of Common Stock.

 SECTION 3.4.  EFFECT OF CERTAIN TRANSACTIONS.  The number of shares of Common
Stock reserved for the Plan pursuant to Section 3.1, the maximum number of
shares of Common Stock offered pursuant to Section 3.2(b), and the determination
under Section 3.3 of the purchase price per share of the shares of Common Stock
offered to Participants pursuant to an Offering shall be appropriately adjusted
to reflect any increase or decrease in the number of issued shares of Common
Stock resulting from a stock split, a consolidation of shares, the payment of a
stock dividend, or any other capital adjustment affecting the number of issued
shares of Common Stock. In the event that the outstanding shares of Common Stock
shall be changed into or exchanged for a different number or kind of shares of
stock or other securities of the Company or another corporation, whether through
reorganization, recapitalization, merger, consolidation, or otherwise, then
there shall be substituted for each share of Common Stock reserved for issuance
under the Plan but not yet purchased by Participants, the number and kind of
shares of stock or other securities into which each outstanding share of Common
Stock shall be so changed or for which each such share shall be exchanged.

ARTICLE IV

PAYROLL DEDUCTIONS

 SECTION 4.1.  PAYROLL DEDUCTION ELECTIONS.  Any Employee eligible to
participate in the Plan may elect to have the Company deduct from the
Compensation payable to such Employee during each Offering Period any amount
between one percent (1%) and fifteen percent (15%) of such Participant’s
Compensation, in whole multiples of one percent (1%). Such election shall be
made during the thirty day period preceding the Offering Period to which it
first relates. Such election shall become effective as of the first day of such
Participant’s first pay period that begins on or after the first day of such
Offering Period and shall remain

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effective for each successive pay period and for each subsequent Offering until
changed or terminated pursuant to this Article IV. The percentage deduction
specified by the Participant will be deducted from each payment of Compensation
made to the Participant.

 SECTION 4.2.  ELECTION TO INCREASE OR DECREASE PAYROLL DEDUCTIONS.  Subject to
Section 4.4, a Participant who has a payroll deduction election in effect under
Section 4.1 may prospectively increase or decrease during an Offering Period the
percentage amount of the deductions being made by the Company from such
Participant’s Compensation (including a decrease to zero) by delivering to the
Company written direction to make such change. Such change shall become
effective as soon as practicable after the Company’s receipt of such written
direction and shall remain in effect until changed or terminated pursuant to
this Article IV. A Participant shall be permitted to increase or decrease the
percentage amount of the deductions being made from such Participant’s
Compensation only once during each of the portions of an Offering Period that
ends on a Purchase Date; provided, however, a Participant may terminate the
deductions being made from such Participant’s Compensation at any time during
such Offering Period. If a Participant terminates deductions, such Participant
cannot resume deductions during that Offering Period.

 SECTION 4.3.  TERMINATION OF ELECTION UPON TERMINATION OF EMPLOYMENT.  The
termination of employment of a Participant for any reason shall automatically
terminate the election of such Participant to have amounts deducted from such
Participant’s Compensation pursuant to this Article IV that is then in effect.
Such termination shall be effective immediately following the pay period during
which such termination of employment occurs, but shall not affect the deduction
from Compensation for that pay period.

 SECTION 4.4.  FORM OF ELECTIONS.  Except as otherwise permitted by the Company,
any election by a Participant regarding participation in or withdrawal from the
Plan or deductions from Compensation pursuant to this Article IV shall be in
writing on a form furnished by the Company for such purpose and shall be made by
having such Participant file such form with the Company in the manner prescribed
from time to time by the Company.

ARTICLE V

STOCK PURCHASE ACCOUNTS AND PURCHASE OF COMMON STOCK

 SECTION 5.1.  STOCK PURCHASE ACCOUNTS.  A Stock Purchase Account shall be
established and maintained on the books and records of the Company for each
Participant. Amounts deducted from a Participant’s Compensation pursuant to
Article IV shall be credited to such Participant’s Stock Purchase Account. No
interest or other increment shall accrue or be payable to any Participant with
respect to any amounts credited to such Stock Purchase Accounts. All amounts
credited to such Stock Purchase Accounts shall be withdrawn, paid, or applied
toward the purchase of Common Stock pursuant to the provisions of this
Article V.

 SECTION 5.2.  PURCHASE OF COMMON STOCK.

(a)                                GENERAL.  As of each Purchase Date, the
amount to the credit of a Participant in such Participant’s Stock Purchase
Account shall be used to purchase from the Company on such Participant’s behalf
the largest number of whole shares of Common Stock which can be purchased at the
price determined under Section 3.3 with the amount then credited to such
Participant’s Stock Purchase Account, subject to the limitations set forth in
Article III on the maximum number of shares of Common Stock such Participant may
purchase. As of such date, such Participant’s Stock Purchase Account shall be
charged with the aggregate purchase price of the shares of Common Stock
purchased on such Participant’s behalf. No brokerage or other fees are to be
charged upon a purchase. Stock transfer taxes, if any, shall be paid by the
Company. The remaining balance, if any, credited to such Participant’s Stock
Purchase Account shall be carried forward and used to purchase shares of Common
Stock on the next succeeding Purchase Date; provided that any excess balance
remaining in a Participant’s Stock Purchase Account after the application of the
limitations in Section 3.2 shall be refunded to the Participant.

(b)                               ISSUANCE OF COMMON STOCK.  The shares of
Common Stock purchased for a Participant as of a Purchase Date shall be deemed
to have been issued by the Company for all purposes as of the close of business
on such date. Prior to such date, none of the rights and privileges of a
stockholder of the Company shall exist with respect to such shares of Common
Stock. As soon as practicable after such a Purchase Date the Company shall issue
and deliver, or shall cause its stock transfer agent to issue and deliver, a
certificate for the number of shares of Common Stock purchased for a
Participant, which certificate shall be issued in the Participant’s name or, if
so specified by the Participant, in the name of the Participant and such other
person as the Participant shall

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designate as joint tenants with right of survivorship. In lieu of issuing a
certificate, the Company may elect to deliver to the Participant a statement
which shall indicate the number of shares of Common Stock purchased for such
Participant and the aggregate number of shares of Common Stock held on behalf of
such Participant under the Plan.

(c)                                INSUFFICIENT COMMON STOCK AVAILABLE.  If, as
of any Purchase Date, the aggregate Stock Purchase Accounts available for the
purchase of shares of Common Stock pursuant to Section 5.2(a) would purchase a
number of shares of Common Stock in excess of the number of shares of Common
Stock then available for purchase under the Plan, (i) the number of shares of
Common Stock which would otherwise be purchased for each Participant on such
date shall be reduced proportionately to the extent necessary to eliminate such
excess, (ii) the remaining balance to the credit of each Participant in each
such Participant’s Stock Purchase Accounts shall be distributed to each such
Participant, and (iii) the Plan shall terminate automatically upon the
distribution of the remaining balance in such Stock Purchase Accounts.

 SECTION 5.3.  WITHDRAWAL FROM PLAN PRIOR TO PURCHASE OF COMMON STOCK.  In the
event (i) a Participant elects in writing for any reason to withdraw from the
Plan during an Offering Period or (ii) a Participant’s employment with the
Company terminates for any reason prior to the end of an Offering Period, then
the entire amount remaining to the credit of such Participant in such
Participant’s Stock Purchase Account shall be distributed to such Participant
(or, if such Participant is deceased, to such Participant’s Beneficiary) as soon
as administratively practicable after such withdrawal or termination of
employment (as the case may be).

ARTICLE VI

COMMITTEE

 SECTION 6.1.  POWERS OF THE COMMITTEE.  The Committee shall administer the
Plan. The Committee shall have all powers necessary to enable it to carry out
its duties under the Plan properly. Not in limitation of the foregoing, the
Committee shall have the power to construe and interpret the Plan and to
determine all questions that shall arise thereunder. The decision of the
Committee upon all matters within the scope of its authority shall be final and
conclusive on all persons, except to the extent otherwise provided by law.

 SECTION 6.2.  INDEMNIFICATION OF THE COMMITTEE.  The Company agrees to
indemnify and hold harmless the members of the Committee against any
liabilities, loss, costs, or damage that they may incur in acting as such
members and to assume the defense of any and allocations, suits, or proceedings
against the members of the Committee, to the extent permitted by applicable law.

ARTICLE VII

AMENDMENT AND TERMINATION

 SECTION 7.1.  AMENDMENT OF THE PLAN.  The Company expressly reserves the right,
at any time and from time to time, to amend in whole or in part any of the terms
and provisions of the Plan; provided, however, no amendment may without the
approval of the shareholders of the Company increase the number of shares of
Common Stock reserved under the Plan.

 SECTION 7.2.  TERMINATION OF PLAN.  The Company expressly reserves the right,
at any time and for whatever reason it may deem appropriate, to terminate the
Plan. The Plan shall continue in effect until terminated pursuant to (i)  the
preceding sentence or (ii)  Section 5.2(c). Upon any termination of the Plan,
the entire amount credited to the Stock Purchase Account of each Participant
shall be distributed to each such Participant.

 SECTION 7.3.  PROCEDURE FOR AMENDMENT OR TERMINATION.  Any amendment to the
Plan or termination of the Plan may be retroactive to the extent not prohibited
by applicable law. Any amendment to the Plan or termination of the Plan shall be
made by the Company by resolution of the Board of Directors (subject to
Section 7.1) and shall not require the approval or consent of any Participant or
Beneficiary in order to be effective.

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ARTICLE VIII

MISCELLANEOUS

 SECTION 8.1.  ADOPTION BY A SUBSIDIARY.  A Subsidiary may, with the approval of
the Board of Directors and the board of directors of such Subsidiary, elect to
adopt the Plan as of a date mutually agreeable to the Board of Directors and the
board of directors of such Subsidiary. Any such adoption of the Plan by a
Subsidiary shall be evidenced by an appropriate instrument of adoption executed
by such Subsidiary.

 SECTION 8.2.  AUTHORIZATION AND DELEGATION TO THE BOARD OF DIRECTORS.  Each
Subsidiary that hereafter adopts the Plan authorizes the Board of Directors
(i) to amend or terminate the Plan without further action by said Subsidiary as
provided in Article VII and (ii) to perform such other acts and to do such other
things as the Board of Directors is expressly directed, authorized, or permitted
to perform or do as provided herein.

 SECTION 8.3.  TRANSFERABILITY OF RIGHTS.  Rights under the Plan are not
transferable by a Participant other than by will or the laws of descent and
distribution and are exercisable during a Participant’s lifetime only by the
Participant.

 SECTION 8.4.  NO EMPLOYMENT RIGHTS.  Participation in the Plan shall not give
any employee of the Company or any Subsidiary any right to remain employed or,
upon termination of employment, any right or interest in the Plan, except as
expressly provided herein.

 SECTION 8.5.  COMPLIANCE WITH LAW.  No shares of Common Stock shall be issued
under the Plan prior to compliance by the Company to the satisfaction of its
counsel with any applicable laws.

 SECTION 8.6.  CONSTRUCTION.  Article, Section, and paragraph headings have been
inserted in the Plan for convenience of reference only and are to be ignored in
any construction of the provisions hereof. If any provision of the Plan shall be
invalid or unenforceable, the remaining provisions shall nevertheless be valid,
enforceable, and fully effective. It is the intent that the Plan shall at all
times constitute an “employee stock purchase plan” within the meaning of
Section 423(b) of the Code, and the Plan shall be construed, and interpreted to
remain such. The Plan shall be construed, administered, regulated, and governed
by the laws of the United States to the extent applicable, and to the extent
such laws are not applicable, by the laws of The Commonwealth of Massachusetts.
Without limiting the foregoing, all Participants for an Offering Period shall
have the same rights and privileges with respect to their rights to acquire
Common Stock under the Plan for such period, subject to the express terms
hereof.

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