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corresp

Hogan & Hartson

l.l.p.

    111 south calvert street

    baltimore, md 21202

    tel (410) 659-2700

    fax (410) 539-6981

    www.hhlaw.com

September 7, 2005

VIA FACSIMILE

Jeffrey Riedler

Assistant Director

Securities and Exchange Commission

Division of Corporation Finance

100 F Street, NE, Mail Stop 6010

Washington, DC 20549

    RE:

    Avalon Pharmaceuticals, Inc.

    Amendment No. 3 to Registration Statement on Form S-1

    File No. 333-124565

Dear Mr. Riedler:

     On behalf of Avalon Pharmaceuticals, Inc. (“Avalon” or the “Company”), this letter is in
response to the staff’s letter of comment dated September 7, 2005 to Dr. Kenneth C. Carter, with
respect to the above-referenced Amendment No. 3 to the Company’s Registration Statement on Form S-1
(the “Registration Statement”) and is pursuant to our conversation with Song Brandon and John Krug
on that date.

     After reviewing the comment letter, it appeared that the staff’s primary concerns with the
subordinated line of credit facility the Company is in the process of putting in place is the
ability of the Company to repay any borrowings made under the facility in common stock in its
discretion and the proposed issuance of warrants to the lenders as an inducement to participate in
the credit facility. While we are comfortable that these features do not result in the line of
credit needing to be integrated with the Company’s proposed initial public offering under the
“5-factor test”, primarily because the line as proposed involves no current offer of any common
stock or security convertible into common stock, in an effort to allay the staff’s concerns and
expeditiously resolve the issue, we are proposing to eliminate any equity features from the line of
credit arrangements. We note that the line of credit is subject to conditions that are not yet met
and so is not yet available to the Company, no warrants have been issued thereunder and no
borrowings made. Therefore, it is possible to amend the terms to make these changes without raising
the concerns that the staff has pointed to.

washington, dc     new york     baltimore     northern virginia     miami     los angeles     denver     boulder     colorado springs

berlin     munich     brussels     london     paris     geneva     budapest     warsaw     moscow     beijing     hong kong     shanghai     tokyo

Hogan & Hartson l.l.p.

Mr. Jeffrey Riedler

September 7, 2005

Page 2

     As a result of these changes to the line of credit arrangements, the line of credit will
become a simple loan agreement repayable only in cash, and no warrants will be issued. No
borrowings have been made under it, and none are expected to be made if the IPO is completed in a
timely fashion. Once the IPO is completed, if not drawn upon, the line of credit will expire. To
the extent it is drawn upon, it will be repaid in cash at maturity. As a straight commercial loan
agreement, the line of credit facility does not represent the offer of any security that would be
integrated with the proposed IPO.

     The principal lenders under the line of credit facility are all existing major stockholders of
the Company who have indicated a willingness to provide these funds, if needed by the Company, and
are willing to forego any equity component of the lending facility. We are still in the process of
finalizing lender participation, but the names of all lenders, their committed amounts, and the
names of the stockholders who did not participate in the facility and will have a portion of their
shares of preferred stock converted to common stock will be disclosed in schedules to the line of
credit facility that will be filed.

     We will provide the staff with copies of the revised line of credit agreement to review. We
expect that will be completed in the next several days.

     In the meantime, we would appreciate hearing from you on Thursday, if possible, that you
concur that the line of credit as revised no longer raises the integration issues referred to in
your September 7 letter.

* * * *

     If you have any questions concerning this letter or if you would like any additional
information, please do not hesitate to call me at (212) 918-3651 or Michael J. Silver at (410)
659-2741.

Very truly yours,

Stephanie D. Marks

    cc:

    Kenneth C. Carter, Ph.D.

Gary Lessing

Tom G. David