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                                                                   Exhibit 10.3

                                 ARCHEMIX CORP.
                                300 Third Street
                               Cambridge, MA 02142

September 8, 2006

Dr. James Gilbert
8 Worcester Street
Belmont, MA 02478

Dear Jim:

     I am very pleased to provide you with a summary of the terms, benefits and
conditions of your anticipated employment by Archemix Corp. ("Archemix"). The
following sets forth the proposed terms and conditions of your offer of
employment. We hope that you choose to join the Archemix team and look forward
to a mutually beneficial relationship.

1. POSITION Your initial position will be Sr. Vice President, Clinical and
Regulatory Affairs; Chief Medical Officer. As you progress with Archemix, your
position and assignments are, of course, subject to change. As an Archemix
employee, we expect that you will perform any and all duties and
responsibilities normally associated with your position in a satisfactory manner
and to the best of your abilities at all times. Your performance will be
reviewed on a periodic basis as long as you remain employed by Archemix.

2. STARTING DATE/NATURE OF RELATIONSHIP If you accept this offer, your
employment with Archemix will begin on or about September 25, 2006. You should
report to Errol DeSouza at Archemix at 8:30 a.m. on that date, and you will be
expected to devote all of your working time to the performance of your duties at
Archemix throughout your employment with Archemix. No provision of this letter
shall be construed to create an express or implied employment contract, or a
promise of employment for any specific period of time. Your employment with
Archemix is at-will employment, which may be terminated by you or Archemix at
any time for any reason.

3. COMPENSATION AND BENEFITS Your initial base pay shall be at a gross rate of
$25,000 per month, minus customary deductions for federal and state taxes plus
any elective benefits or deductions. You may be eligible for an annual bonus
target equal to 27% of your base salary, based on overall company and individual
performance. Potential bonus amounts may be compensated in cash. Archemix will
provide you a sign-on bonus for $60,000, minus customary deductions for federal
and state taxes, which will be included in your first paycheck. Subject to
approval by the Board of Directors (or an appropriate Committee appointed by the
Board of Directors), and pursuant to a written stock option agreement entered
into by and between you and Archemix (the "Option Agreement") pursuant to the
Corporation's 2001 Employee, Director and Consultant Stock Plan (the "2001
Plan"), as amended, Archemix will grant you an option to

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purchase 400,000 shares of Archemix Common Stock (the "Option"). The exercise
price of the Option will be the fair market value of the Corporation's Common
Stock on the date the Option is granted and such Option shall be subject to the
terms and conditions of the Option as set forth in the 2001 Plan and the Option
Agreement. To the extent permissible under applicable federal tax law, the
Option will be an incentive stock option with the Option vesting on the
following schedule: twenty-five percent (25%) of such shares shall vest on the
first (1st) anniversary of the date of your option agreement; after the first
(1st) anniversary, the remaining seventy-five percent (75%) of such shares shall
vest ratably in three (3) month periods until the fourth (4th) anniversary your
option agreement. Such vesting shall commence on the first anniversary,
September 25, 2007 and quarterly thereafter.

In addition to your compensation, you may take advantage of various benefits
offered by Archemix, including group medical plans and paid vacation time. These
benefits, of course, may be modified or changed from time to time at the sole
discretion of Archemix, and the provision of such benefits to you in no way
changes or impacts your status as an at-will employee. Archemix's present
benefit structure and other important information about the benefits for which
you may be eligible is described in the attached benefits summary sheet and in
the employee handbook that you will receive upon the commencement of your
employment. Where a particular benefit is subject to a formal plan (for example,
medical insurance or life insurance), eligibility to participate in and receive
any particular benefit is governed solely by the applicable plan document.
Should you ever have any questions about Archemix benefits, you should ask the
Human Resources Manager for a copy of the applicable plan document.

4. BEFORE YOU START Your employment with Archemix is conditioned on your
eligibility to work in the United States. On your first day, you must complete
an I-9 Form and provide Archemix with any of the accepted forms of
identification specified on the I-9 Form.

5. CONFIDENTIALITY Archemix considers the protection of its confidential
information, proprietary materials and goodwill to be extremely important. Given
the confidential nature of various aspects of our business, you may not discuss
the fact or terms of this offer or any employment discussions with anyone other
than a member of the Archemix management team and members of your immediate
family (and, if relevant, your recruiting firm, financial advisor or lawyer). In
addition, as is true of all Archemix employees, you will be required to sign an
agreement relating to confidentiality, non-competition, non-solicitation and
work product on your first day of work as a condition of this offer of
employment.

6. MISCELLANEOUS This letter constitutes our entire offer regarding the terms
and conditions of your prospective employment with Archemix. It supersedes any
prior agreements, or other promises or statements (whether oral or written)
regarding the offered terms of employment. The terms of your employment shall be
governed by the law of the Commonwealth of Massachusetts. By accepting this
offer of employment, you agree that any action, demand, claim or counterclaim in
connection with any aspect of your employment with Archemix, or any separation
of employment (whether voluntary or involuntary) from Archemix, shall be
resolved by a judge alone, and you waive and forever renounce your right to a
trial before a civil jury.


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     You may accept this offer of employment and the terms and conditions hereof
by signing the enclosed additional copy of this letter. Your signature on the
copy of this letter and your submission of the signed copy to me will evidence
your agreement with the terms and conditions set forth herein. This offer will
expire on September 15, 2006, unless accepted by you prior to such date.

     We are excited to offer you the opportunity to join Archemix, and we look
forward to having you aboard. We are pleased that you have chosen to join the
Archemix team, and confident that you will make an important contribution to our
unique and exciting enterprise.

                                        Sincerely,


                                        Errol DeSouza
                                        ---------------------------------------
                                        President & Chief Executive Officer

Acknowledgment:

     I ____________________________ have read, understand, and accept employment
on the terms and conditions outlined in this letter. I am not relying on any
representations made to me by anyone other than as set forth above.


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Signature

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Date


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