EX-10.2






Exhibit 10.2 — REGISTRATION RIGHTS AGREEMENT




This Registration Rights Agreement (the “Agreement”) is made and entered into as of this
27th day of February, 2006 by and among Avalon Pharmaceuticals, Inc., a Delaware
corporation (the “Company”), and the “Investors” executing this Agreement and named in that certain
Purchase Agreement by and among the Company and the Investors dated the date hereof (the “Purchase
Agreement”).



The parties hereby agree as follows:



1. Certain Definitions.



As used in this Agreement, the following terms shall have the following meanings:



“Affiliate” means, with respect to any person, any other person which directly or
indirectly controls, is controlled by, or is under common control with, such person.



“Business Day” means a day, other than a Saturday or Sunday, on which banks in New
York City and San Francisco, California are open for the general transaction of business.



“Common Stock” shall mean the Company’s common stock, par value $0.01 per share, and
any securities into which such shares may hereinafter be reclassified.



“Investors” shall mean the Investors identified in the Purchase Agreement and any
Affiliate or permitted transferee of any Investor who is a subsequent holder of any Registrable
Securities.



“Prospectus” shall mean the prospectus included in any Registration Statement, as
amended or supplemented by any prospectus supplement, with respect to the terms of the offering of
any portion of the Registrable Securities covered by such Registration Statement and by all other
amendments and supplements to the prospectus, including post-effective amendments and all material
incorporated by reference in such prospectus.



“Register,” “registered” and “registration” refer to a registration
made by preparing and filing a Registration Statement or similar document in compliance with the
1933 Act (as defined below), and the declaration or ordering of effectiveness of such Registration
Statement or document.



“Registrable Securities” shall mean (i) the Shares, and (ii) any other securities
issued or issuable with respect to or in exchange for Registrable Securities; provided, that, a
security shall cease to be a Registrable Security upon (A) sale pursuant to a Registration
Statement or Rule 144 under the 1933 Act, or (B) such security becoming eligible for sale by the
Investors pursuant to Rule 144(k).



“Registration Statement” shall mean any registration statement of the Company filed
under the 1933 Act that covers the resale of any of the Registrable Securities pursuant to the
provisions of this Agreement (including each of the Registration Statements referred to in Section
2), amendments and supplements to such Registration Statement(s), including post-effective
amendments, all exhibits and all material filed and incorporated by reference in such Registration
Statement.



“Required Investors” mean the Investors holding a majority of the Registrable
Securities.



“Rule 401”, “Rule 415”, “Rule 416”, “Rule 429” and “Rule
461” mean Rule 401, Rule 415, Rule 416, Rule 429 and Rule 461, respectively, each as
promulgated by the SEC pursuant to the 1933 Act, as such Rule may be amended from time to time, or
any similar rule or regulation hereafter adopted by the SEC having substantially the same effect as
such Rule.



“SEC” means the U.S. Securities and Exchange Commission.” 



“Shares” means the shares of Common Stock issued pursuant to the Purchase Agreement.



“1933 Act” means the Securities Act of 1933, as amended, and the rules and regulations
promulgated thereunder.



“1934 Act” means the Securities Exchange Act of 1934, as amended, and the rules and
regulations promulgated thereunder.



2. Registration.



(a) Registration Statements.



(i) Promptly following the closing of the purchase and sale of the securities contemplated by
the Purchase Agreement (the “Closing Date”) but no later than five (5) Business Days after the
filing of the Company’s Annual Report on Form 10-K for the year ended December 31, 2005 (the “S-1
Filing Deadline”), the Company shall prepare and file with the SEC a “shelf” registration statement
covering all Registrable Securities for a secondary or resale offering to be made on a continuous
basis pursuant to Rule 415. Such registration statement shall be on Form S-1 (the “S-1 Registration
Statement”) and shall include the plan of distribution attached hereto as Exhibit A. Such
S-1 Registration Statement also shall cover, to the extent allowable under the 1933 Act and the
rules promulgated thereunder (including Rule 416), such indeterminate number of additional shares
of Common Stock resulting from stock splits, stock dividends or similar transactions with respect
to the Registrable Securities. Such S-1 Registration Statement shall not include any shares of
Common Stock or other securities for the account of any other holder without the prior written
consent of the Required Investors, except for shares of Common Stock held by the Company’s
stockholders having “piggyback” registration rights expressly set forth in registration rights
agreements entered into by the Company prior to the date hereof. A copy of the initial filing of
the Registration Statement (and each pre-effective amendment thereto) shall be provided to the
Investors and their counsel prior to filing. If the S-1 Registration Statement covering the
Registrable Securities is not filed with the SEC on or prior to the S-1 Filing Deadline, the
Company will make pro rata payments to each Investor, as liquidated damages and not as a penalty,
in an amount equal to 1.5% of the aggregate amount invested by such Investor for each 30-day period
or pro rata for any portion thereof following the Filing Deadline for which the S-1 Registration
Statement is filed with respect to the Registrable Securities. Such payments shall constitute the
Investors’ exclusive monetary remedy for such events, but shall not affect the right of the
Investors to seek injunctive relief. Payments to be made pursuant to this Section 2(a)(i) shall be
due and payable immediately upon demand in immediately available cash funds. The parties agree that
the liquidated damages provided for in this Section 2(a)(i) represent a reasonable estimate on the
part of the parties, as of the date of this Agreement, of the amount of damages that may be
incurred by the Investors if the S-1 Registration Statement is not filed by the S-1 Filing
Deadline.



(ii) Filing of, or Conversion to, Registration Statement on Form S-3. Within fifteen
(15) calendar days after the Company shall be eligible to file a registration statement under the
1933 Act to register on Form S-3 the Registrable Securities for resale but no later than December
15, 2006 (the “S-3 Filing Deadline”), the Company shall prepare and file with the SEC a “shelf”
registration statement covering all the Registrable Securities for a secondary or resale offering
to be made on a continuous basis pursuant to Rule 415. Such registration statement (in any of the
following cases referred to as the “S-3 Registration Statement”) shall be (A) on Form S-3 (if, and
only if, the Company is permitted under the 1933 Act and the rules promulgated thereunder to file a
registration statement on Form S-3), (B) a pre-effective amendment to the S-1 Registration
Statement if the S-1 Registration Statement has not previously been declared effective by the SEC,
or (C) a post-effective amendment to the S-1 Registration Statement on Form S-3 if (and only if)
the S-1 Registration Statement has previously been declared effective by the SEC and the Company is
then permitted under the 1933 Act and the rules promulgated thereunder (including Rule 401) to file
a post-effective amendment to such S-1 Registration Statement on Form S-3. Such S-3 Registration
Statement also shall cover, to the extent allowable under the 1933 Act and the rules promulgated
thereunder (including Rule 416), such indeterminate number of additional shares of Common Stock
resulting from stock splits, stock dividends or similar transactions with respect to the
Registrable Securities. Such S-3 Registration Statement shall not include any shares of Common
Stock or other securities for the account of any other holder without the prior written consent of
the Required Investors, except for shares of Common Stock held by the Company’s stockholders having
“piggyback” registration rights expressly set forth in registration rights agreements entered into
by the Company prior to the date hereof. The initial filing of the S-3 Registration Statement
shall be provided to the Investors and their counsel prior to its filing. If the S-3 Registration
Statement is a new registration statement covering the Registrable Securities filed with the SEC
pursuant to Clause (A) of the second sentence of this Section 2(a)(ii) and the Company is not
permitted pursuant to Rule 429 to use the prospectus included in the S-3 Registration Statement as
a combined prospectus for the offering covered by the S-1 Registration Statement, the Company shall
use commercially reasonable efforts to remove from registration by means of a post-effective
amendment to the S-1 Registration Statement any of the Registrable Securities registered under the
S-1 Registration Statement that remain unsold at the time the S-3 Registration Statement is
declared effective by the SEC and cause such post-effective amendment to be declared effective by
the SEC no earlier than concurrently with the effectiveness of the S-3 Registration Statement. If
the S-3 Registration Statement is not filed with the SEC by the S-3 Filing Deadline (unless the
Company is not then eligible to make a filing on Form S-3), the Company will make pro rata payments
to each Investor, as liquidated damages and not as a penalty, in an amount equal to 1.5% of the
aggregate amount invested by such Investor for each 30-day period or pro rata for any portion
thereof following the date by which such Registration Statement should have been filed for which no
S-3 Registration Statement is filed with respect to the Registrable Securities. Such payments
shall constitute the Investors’ exclusive monetary remedy for such events, but shall not affect the
right of the Investors to seek injunctive relief. Payments to be made pursuant to this Section
2(a)(ii) shall be due and payable immediately upon demand in immediately available cash funds. The
parties agree that the liquidated damages provided for in this Section 2(a)(ii) represent a
reasonable estimate on the part of the parties, as of the date of this Agreement, of the amount of
damages that may be incurred by the Investors if the S-3 Registration Statement is not filed by the
S-3 Filing Deadline.



(b) Expenses. The Company will pay all expenses associated with each registration,
including filing and printing fees, the Company’s counsel and accounting fees and expenses, costs
associated with clearing the Registrable Securities for sale under applicable state securities
laws, listing fees, reasonable out-of-pocket fees and expenses of one counsel to the Investors
(which fees and expenses shall not exceed $15,000 in the aggregate) and the Investors’ reasonable
out-of-pocket expenses in connection with the registration, but excluding discounts, commissions,
fees of underwriters, selling brokers, dealer managers or similar securities industry professionals
with respect to the Registrable Securities being sold.



(c) Effectiveness.



(i) The Company shall use commercially reasonable efforts to have the Registration
Statement(s) declared effective as soon as practicable (including filing with the SEC a request for
acceleration of its effectiveness in accordance with Rule 461 within five (5) Business Days of the
date that the Company is notified (orally or in writing, whichever is earlier) by the staff of the
SEC that a Registration Statement will not be reviewed, or not be subject to further review). The
Company shall notify the Investors by facsimile or e-mail as promptly as practicable, and in any
event, within twenty-four (24) hours, after any Registration Statement is declared effective and
shall simultaneously provide the Investors with copies of any related Prospectus to be used in
connection with the sale or other disposition of the securities covered thereby. If (A) the S-1
Registration Statement or the S-3 Registration Statement is not declared effective by the SEC prior
to five (5) Business Days after the staff of the SEC shall have informed the Company (orally or in
writing, whichever is earlier) that such Registration Statement will not be reviewed by the staff
of the SEC or not be subject to further review, or (B) after a Registration Statement has been
declared effective by the SEC, sales cannot be made pursuant to such Registration Statement for any
reason (including without limitation by reason of a stop order, or the Company’s failure to update
the Registration Statement), but excluding the inability of any Investor to sell the Registrable
Securities covered thereby due to market conditions and except as excused pursuant to Section
2(c)(ii) below, then the Company will make pro rata payments to each Investor, as liquidated
damages and not as a penalty, in an amount equal to 1.5% of the aggregate amount invested by such
Investor for each 30- day period or pro rata for any portion thereof following the date by which
such Registration Statement should have been effective (the “Blackout Period”). Such payments
shall constitute the Investors’ exclusive monetary remedy for such events, but shall not affect the
right of the Investors to seek injunctive relief. The amounts payable as liquidated damages
pursuant to this paragraph shall be paid monthly within three (3) Business Days of the last day of
each month following the commencement of the Blackout Period until the termination of the Blackout
Period. Such payments shall be made to each Investor in cash. The parties agree that the
liquidated damages provided for in this Section 2(c)(i) represent a reasonable estimate on the part
of the parties, as of the date of this Agreement, of the amount of damages that may be incurred by
the Investors if the S-1 Registration Statement is not declared effective as hereinabove provided
or if the S-3 Registration Statement is not declared effective by the applicable S-3 Filing
Deadline. For purposes of the obligations of the Company under this Agreement, except in the case
of any Investors who elect in writing not to have its Registrable Securities included in the
Registration Statement, no Registration Statement shall be considered “effective” with respect to
any Registrable Securities unless such Registration Statement lists the Investors of such
Registrable Securities as “Selling Stockholders” and includes such other information as is required
to be disclosed with respect to such Investors to permit them to sell their Registrable Securities
pursuant to such Registration Statement.



(ii) For not more than thirty (30) consecutive days or for a total of not more than sixty (60)
days in any twelve (12) month period, the Company may delay the disclosure of material non-public
information concerning the Company, by suspending the use of any Prospectus included in any
registration contemplated by this Section or by delaying any post-effective amendment to the Form
S-1 Registration Statement (if the Form S-3 Registration Statement has not yet become effective),
if such disclosure at the time is not, in the good faith opinion of the Company, in the best
interests of the Company (an “Allowed Delay”); provided, that the Company shall promptly (a) notify
the Investors in writing of the existence of (but in no event, without the prior written consent of
an Investor, shall the Company disclose to such Investor any of the facts or circumstances
regarding)an Allowed Delay, (b) advise the Investors in writing to cease all sales under the
Registration Statement until the end of the Allowed Delay and (c) use commercially reasonable
efforts to terminate an Allowed Delay as promptly as practicable.



3. Company Obligations. The Company will use commercially reasonable efforts to
effect the registration of the Registrable Securities in accordance with the terms hereof, and
pursuant thereto the Company will, as expeditiously as possible (but subject to Section 2(c)(ii)):



(a) use commercially reasonable efforts to cause such Registration Statement to become
effective and (subject to the provisions of Section 2(a)(ii) regarding removal from registration by
means of a post-effective amendment to the S-1 Registration Statement any of the Registrable
Securities registered under the S-1 Registration Statement that remain unsold at the time the S-3
Registration Statement is declared effective), to remain continuously effective for a period that
will terminate upon the earlier of (i) the date on which all Registrable Securities covered by such
Registration Statement as amended from time to time, have been sold, and (ii) the date on which all
Registrable Securities covered by such Registration Statement may be sold pursuant to Rule 144(k)
(the “Effectiveness Period”) and advise the Investors in writing when the Effectiveness Period has
expired;



(b) prepare and file with the SEC such amendments and post-effective amendments to the
Registration Statement and the Prospectus as may be necessary to keep the Registration Statement
effective for the Effectiveness Period and to comply with the provisions of the 1933 Act and the
1934 Act with respect to the distribution of all of the Registrable Securities covered thereby;



(c) use commercially reasonable efforts to (i) prevent the issuance of any stop order or other
suspension of effectiveness and, (ii) if such order is issued, obtain the withdrawal of any such
order at the earliest possible moment;



(d) prior to any public offering of Registrable Securities, use commercially reasonable
efforts to register or qualify or cooperate with the Investors and their counsel in connection with
the registration or qualification of such Registrable Securities for offer and sale under the
securities or blue sky laws of such jurisdictions requested by the Investors and do any and all
other commercially reasonable acts or things necessary or advisable to enable the distribution in
such jurisdictions of the Registrable Securities covered by the Registration Statement; provided,
however, that the Company shall not be required in connection therewith or as a condition thereto
to (i) qualify to do business in any jurisdiction where it would not otherwise be required to
qualify but for this Section 3(d), (ii) subject itself to general taxation in any jurisdiction
where it would not otherwise be so subject but for this Section 3(d), or (iii) file a general
consent to service of process in any such jurisdiction;



(e) use commercially reasonable efforts to cause all Registrable Securities covered by a
Registration Statement to be listed on each securities exchange, interdealer quotation system or
other market on which similar securities issued by the Company are then listed;



(f) promptly notify the Investors, at any time when a Prospectus relating to Registrable
Securities is required to be delivered under the 1933 Act (including during any period when the
Company is in compliance with Rule 172), upon discovery that, or upon the happening of any event as
a result of which, the Prospectus included in a Registration Statement, as then in effect, includes
an untrue statement of a material fact or omits to state any material fact required to be stated
therein or necessary to make the statements therein not misleading in light of the circumstances
then existing, and at the request of any such holder, promptly prepare, file with the SEC pursuant
to Rule 172 and furnish to such holder a supplement to or an amendment of such Prospectus as may be
necessary so that such Prospectus shall not include an untrue statement of a material fact or omit
to state a material fact required to be stated therein or necessary to make the statements therein
not misleading in light of the circumstances then existing; and



(g) otherwise use commercially reasonable efforts to comply with all applicable rules and
regulations of the SEC under the 1933 Act and the 1934 Act, including Rule 172, notify the
Investors promptly if the Company no longer satisfies the conditions of Rule 172 and take such
other actions as may be reasonably necessary to facilitate the registration of the Registrable
Securities hereunder; and make available to its security holders, as soon as reasonably
practicable, but not later than the Availability Date (as defined below), an earnings statement
covering a period of at least twelve (12) months, beginning after the effective date of each
Registration Statement, which earnings statement shall satisfy the provisions of Section 11(a) of
the 1933 Act, including Rule 158 promulgated thereunder (for the purpose of this Section 3(g),
“Availability Date” means the 45th day following the end of the fourth fiscal quarter that includes
the effective date of such Registration Statement, except that, if such fourth fiscal quarter is
the last quarter of the Company’s fiscal year, “Availability Date” means the 90th day after the end
of such fourth fiscal quarter).



(h) With a view to making available to the Investors the benefits of Rule 144 (or its
successor rule) and any other rule or regulation of the SEC that may at any time permit the
Investors to sell shares of Common Stock to the public without registration, the Company covenants
and agrees to: (i) make and keep public information available, as those terms are understood and
defined in Rule 144, until the earlier of (A) six months after such date as all of the Registrable
Securities may be resold pursuant to Rule 144(k) or any other rule of similar effect or (B) such
date as all of the Registrable Securities shall have been resold; (ii) file with the SEC in a
timely manner all reports and other documents required of the Company under the 1934 Act; and (iii)
furnish to each Investor upon request, as long as such Investor owns any Registrable Securities,
(A) a written statement by the Company that it has complied with the reporting requirements of the
1934 Act, and (B) such other information as may be reasonably requested in order to avail such
Investor of any rule or regulation of the SEC that permits the selling of any such Registrable
Securities without registration.



(i) With a view to satisfying its obligations under Section 2(a)(ii), the Company:



(i) represents and warrants that (A) since November 14, 2005 through the date of this
Agreement, it has filed with the SEC in a timely manner all reports and other documents required of
the Company under the 1934 Act (other than a report that is required solely pursuant to Item 1.01,
1.02, 2.03, 2.04, 2.05, 2.06, 4.02(a), 6.01, 6.03 or 6.05 of SEC Form 8-K) and (B) neither the
Company nor any of its consolidated or unconsolidated subsidiaries have, since the end of the last
fiscal year for which certified financial statements of the Company and its consolidated
subsidiaries were included in a report filed pursuant to Section 13(a) or 15(d) of the 1934 Act
through the date of this Agreement: (1) failed to pay any dividend or sinking fund installment on
preferred stock; or (2) defaulted (x) on any installment or installments on indebtedness for
borrowed money, or (y) on any rental on one or more long term leases, which defaults in the
aggregate are material to the financial position of the Company and its consolidated and
unconsolidated subsidiaries, taken as a whole.



(ii) covenants and agrees that (A) from the date of this Agreement through the effective date
of S-3 Registration Statement, it will file with the SEC in a timely manner all reports and other
documents required of the Company under the 1934 Act (other than a report that is required solely
pursuant to Item 1.01, 1.02, 2.03, 2.04, 2.05, 2.06, 4.02(a), 6.01, 6.03 or 6.05 of SEC Form 8-K)
and (B) neither the Company nor any of its consolidated or unconsolidated subsidiaries will, from
the end of the last fiscal year for which certified financial statements of the Company and its
consolidated subsidiaries are included in a report filed pursuant to Section 13(a) or 15(d) of the
1934 Act through the effective date of the S-3 Registration Statement: (1) fail to pay any dividend
or sinking fund installment on preferred stock; or (2) default (x) on any installment or
installments on indebtedness for borrowed money, or (y) on any rental on one or more long term
leases, which default in the aggregate will be material to the financial position of the Company
and its consolidated and unconsolidated subsidiaries, taken as a whole.



4. Due Diligence Review; Information. Upon reasonable prior notice, the Company shall
make available, during normal business hours, for inspection and review by the Investors, advisors
to and representatives of the Investors (who may or may not be affiliated with the Investors and
who are reasonably acceptable to the Company), all financial and other records, all SEC Filings (as
defined in the Purchase Agreement) and other filings with the SEC, and all other corporate
documents and properties of the Company as may be reasonably necessary for the purpose of such
review, and cause the Company’s officers, directors and employees, within a reasonable time period,
to supply all such information reasonably requested by the Investors or any such representative,
advisor or underwriter in connection with such Registration Statement (including, without
limitation, in response to all questions and other inquiries reasonably made or submitted by any of
them), prior to and from time to time after the filing and effectiveness of the Registration
Statement for the sole purpose of enabling the Investors and such representatives, advisors and
underwriters and their respective accountants and attorneys to conduct initial and ongoing due
diligence with respect to the Company and the accuracy of such Registration Statement.



The Company shall not disclose material nonpublic information to the Investors, or to advisors
to or representatives of the Investors, unless prior to disclosure of such information the Company
identifies such information as being material nonpublic information and provides the Investors,
such advisors and representatives with the opportunity to accept or refuse to accept such material
nonpublic information for review and any Investor wishing to obtain such information enters into an
appropriate confidentiality agreement with the Company with respect thereto.



5. Obligations of the Investors.



(a) Each Investor shall promptly furnish in writing to the Company such information regarding
itself, the Registrable Securities held by it and the intended method of disposition of the
Registrable Securities held by it, as shall be reasonably required to effect the registration of
such Registrable Securities and shall execute such documents in connection with such registration
as the Company may reasonably request. At least seven (7) Business Days prior to the first
anticipated filing date of any Registration Statement, the Company shall notify each Investor of
the information the Company requires from such Investor if such Investor elects to have any of the
Registrable Securities included in the Registration Statement. An Investor shall provide such
information to the Company at least three (3) Business Days prior to the first anticipated filing
date of such Registration Statement if such Investor elects to have any of the Registrable
Securities included in the Registration Statement.



(b) Each Investor, by its acceptance of the Registrable Securities agrees to cooperate with
the Company as reasonably requested by the Company in connection with the preparation and filing of
a Registration Statement hereunder, unless such Investor has notified the Company in writing of its
election to exclude all of its Registrable Securities from such Registration Statement.



(c) Each Investor agrees that, upon receipt of any notice from the Company of either (i) the
commencement of an Allowed Delay pursuant to Section 2(c)(ii) or (ii) the happening of an event
pursuant to Section 3(f) hereof, such Investor will immediately discontinue disposition of
Registrable Securities pursuant to the Registration Statement covering such Registrable Securities,
until the Investor is advised by the Company that a supplemented or amended prospectus has been
filed with the SEC and until any related post-effective amendment is declared effective and, if so
directed by the Company, the Investor shall deliver to the Company or destroy (and deliver to the
Company a certificate of destruction) all copies in the Investor’s possession of the Prospectus
covering the Registrable Securities current at the time of receipt of such notice.



6. Indemnification.



(a) Indemnification by the Company. The Company will indemnify and hold harmless each
Investor and its officers, directors, members, employees, attorneys and agents, successors and
assigns, and each other person, if any, who controls such Investor within the meaning of the 1933
Act, against any losses, claims, damages or liabilities, joint or several, to which they may become
subject under the 1933 Act or otherwise, insofar as such losses, claims, damages or liabilities (or
actions in respect thereof) arise out of or are based upon: (i) any untrue statement or alleged
untrue statement of any material fact contained in any Registration Statement, any preliminary
prospectus or final prospectus contained therein, or any amendment or supplement thereof; (ii) any
blue sky application or other document executed by the Company specifically for that purpose or
based upon written information furnished by the Company filed in any state or other jurisdiction in
order to qualify any or all of the Registrable Securities under the securities laws thereof (any
such application, document or information herein called a “Blue Sky Application”); (iii) 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; (iv) any violation by the Company or its
agents of any rule or regulation promulgated under the 1933 Act applicable to the Company or its
agents and relating to action or inaction required of the Company in connection with such
registration; or (v) any failure to register or qualify the Registrable Securities included in any
such Registration in any state where the Company or its agents has affirmatively undertaken or
agreed in writing that the Company will undertake such registration or qualification on an
Investor’s behalf and will reimburse such Investor, and each such officer, director or member and
each such controlling person for any legal or other expenses reasonably incurred by them in
connection with investigating or defending any such loss, claim, damage, liability or action;
provided, however, that the Company will not be liable in any such case if and to
the extent that any such loss, claim, damage or liability arises out of or is based upon an untrue
statement or alleged untrue statement or omission or alleged omission so made in conformity with
information furnished by such Investor or any such controlling person in writing specifically for
use in such Registration Statement or Prospectus.



(b) Indemnification by the Investors. Each Investor agrees, severally but not
jointly, to indemnify and hold harmless, to the fullest extent permitted by law, the Company, its
directors, officers, employees, stockholders and each person who controls the Company (within the
meaning of the 1933 Act) against any losses, claims, damages, liabilities and expense (including
reasonable attorney fees) resulting from any untrue statement of a material fact or any omission of
a material fact required to be stated in the Registration Statement or Prospectus or preliminary
prospectus or amendment or supplement thereto or necessary to make the statements therein not
misleading, to the extent, but only to the extent that such untrue statement or omission is
contained in any information furnished in writing by such Investor to the Company specifically for
inclusion in such Registration Statement or Prospectus or amendment or supplement thereto. In no
event shall the liability of an Investor be greater in amount than the dollar amount of the
proceeds (net of all expense paid by such Investor in connection with any claim relating to this
Section 6 and the amount of any damages such Investor has otherwise been required to pay by reason
of such untrue statement or omission) received by such Investor upon the sale of the Registrable
Securities included in the Registration Statement giving rise to such indemnification obligation.



(c) Conduct of Indemnification Proceedings. Any person entitled to indemnification
hereunder shall (i) give prompt notice to the indemnifying party of any claim with respect to which
it seeks indemnification and (ii) permit such indemnifying party to assume the defense of such
claim with counsel reasonably satisfactory to the indemnified party; provided that any
person entitled to indemnification hereunder shall have the right to employ separate counsel and to
participate in the defense of such claim, but the fees and expenses of such counsel shall be at the
expense of such person unless (a) the indemnifying party has agreed to pay such fees or expenses,
or (b) the indemnifying party shall have failed to assume the defense of such claim and employ
counsel reasonably satisfactory to such person or (c) in the reasonable judgment of any such
person, based upon written advice of its counsel, a conflict of interest exists between such person
and the indemnifying party with respect to such claims (in which case, if the person notifies the
indemnifying party in writing that such person elects to employ separate counsel at the expense of
the indemnifying party, the indemnifying party shall not have the right to assume the defense of
such claim on behalf of such person); and provided, further, that the failure of
any indemnified party to give notice as provided herein shall not relieve the indemnifying party of
its obligations hereunder, except to the extent that such failure to give notice shall materially
adversely affect the indemnifying party in the defense of any such claim or litigation. It is
understood that the indemnifying party shall not, in connection with any proceeding in the same
jurisdiction, be liable for fees or expenses of more than one separate firm of attorneys at any
time for all such indemnified parties. No indemnifying party will, except with the consent of the
indemnified party, consent to entry of any judgment or enter into any settlement that does not
include as an unconditional term thereof the giving by the claimant or plaintiff to such
indemnified party of a release from all liability in respect of such claim or litigation.



(d) Contribution. If for any reason the indemnification provided for in the preceding
paragraphs (a) and (b) is unavailable to an indemnified party or insufficient to hold it harmless,
other than as expressly specified therein, then the indemnifying party shall contribute to the
amount paid or payable by the indemnified party as a result of such loss, claim, damage or
liability in such proportion as is appropriate to reflect the relative fault of the indemnified
party and the indemnifying party, as well as any other relevant equitable considerations. No
person guilty of fraudulent misrepresentation within the meaning of Section 11(f) of the 1933 Act
shall be entitled to contribution from any person not guilty of such fraudulent misrepresentation.
In no event shall the contribution obligation of a holder of Registrable Securities be greater in
amount than the dollar amount of the proceeds (net of all expenses paid by such holder in
connection with any claim relating to this Section 6 and the amount of any damages such holder has
otherwise been required to pay by reason of such untrue or alleged untrue statement or omission or
alleged omission) received by it upon the sale of the Registrable Securities giving rise to such
contribution obligation.



7. Miscellaneous.



(a) Amendments and Waivers. This Agreement may be amended, modified or waived only by
a writing signed by the Company and the Required Investors; provided that if any such
amendment, modification or waiver would adversely affect in any material respect any Investor or
group of Investors who have comparable rights under this Agreement disproportionately to the other
Investors having such comparable rights, such amendment, modification, or waiver shall also require
the written consent of the Investor(s) so adversely affected.



(b) Notices. All notices and other communications provided for or permitted hereunder
shall be made as set forth in Section 9.4 of the Purchase Agreement.



(c) Assignments and Transfers by Investors. The provisions of this Agreement shall be
binding upon and inure to the benefit of the Investors and their respective successors and assigns.
An Investor may transfer or assign, in whole or from time to time in part, to one or more persons
its rights hereunder in connection with the transfer of Registrable Securities by such Investor to
such person, provided that (i) such Investor complies with all laws applicable thereto and provides
written notice of assignment to the Company promptly after such assignment is effected and (ii) the
transferee agrees in writing to be bound by this Agreement as if it were a party hereto.



(d) Assignments and Transfers by the Company. This Agreement may not be assigned by
the Company (whether by operation of law or otherwise) without the prior written consent of the
Required Investors, provided, however, that the Company may assign its rights and delegate its
duties hereunder to any surviving or successor corporation in connection with a merger or
consolidation of the Company with another corporation, or a sale, transfer or other disposition of
all or substantially all of the Company’s assets to another corporation, without the prior written
consent of the Required Investors, after notice duly given by the Company to each Investor.



(e) Benefits of the Agreement. The terms and conditions of this Agreement shall inure
to the benefit of and be binding upon the respective permitted successors and assigns of the
parties. Nothing in this Agreement, express or implied, is intended to confer upon any party other
than the parties hereto or their respective successors and assigns any rights, remedies,
obligations, or liabilities under or by reason of this Agreement, except as expressly provided in
this Agreement.



(f) Counterparts; Faxes. This Agreement may be executed in two or more counterparts,
each of which shall be deemed an original, but all of which together shall constitute one and the
same instrument. This Agreement may also be executed via facsimile, which shall be deemed an
original.



(g) Titles and Subtitles. The titles and subtitles used in this Agreement are used
for convenience only and are not to be considered in construing or interpreting this Agreement.



(h) Severability. Any provision of this Agreement that is prohibited or unenforceable
in any jurisdiction shall, as to such jurisdiction, be ineffective to the extent of such
prohibition or unenforceability without invalidating the remaining provisions hereof but shall be
interpreted as if it were written so as to be enforceable to the maximum extent permitted by
applicable law, and any such prohibition or unenforceability in any jurisdiction shall not
invalidate or render unenforceable such provision in any other jurisdiction. To the extent
permitted by applicable law, the parties hereby waive any provision of law which renders any
provisions hereof prohibited or unenforceable in any respect.



(i) Further Assurances. The parties shall execute and deliver all such further
instruments and documents and take all such other actions as may reasonably be required to carry
out the transactions contemplated hereby and to evidence the fulfillment of the agreements herein
contained.



(j) Entire Agreement. This Agreement is intended by the parties as a final expression
of their agreement and intended to be a complete and exclusive statement of the agreement and
understanding of the parties hereto in respect of the subject matter contained herein. This
Agreement supersedes all prior agreements and understandings between the parties with respect to
such subject matter.



(k) Governing Law; Consent to Jurisdiction; Waiver of Jury Trial. This Agreement
shall be governed by, and construed in accordance with, the internal laws of the State of New York
without regard to the choice of law principles thereof. Each of the parties hereto irrevocably
submits to the exclusive jurisdiction of the courts of the State of New York located in New York
County and the United States District Court for the Southern District of New York for the purpose
of any suit, action, proceeding or judgment relating to or arising out of this Agreement and the
transactions contemplated hereby. Service of process in connection with any such suit, action or
proceeding may be served on each party hereto anywhere in the world by the same methods as are
specified for the giving of notices under this Agreement. Each of the parties hereto irrevocably
consents to the jurisdiction of any such court in any such suit, action or proceeding and to the
laying of venue in such court. Each party hereto irrevocably waives any objection to the laying of
venue of any such suit, action or proceeding brought in such courts and irrevocably waives any
claim that any such suit, action or proceeding brought in any such court has been brought in an
inconvenient forum. EACH OF THE PARTIES HERETO WAIVES ANY RIGHT TO REQUEST A TRIAL BY JURY IN ANY
LITIGATION WITH RESPECT TO THIS AGREEMENT AND REPRESENTS THAT COUNSEL HAS BEEN CONSULTED
SPECIFICALLY AS TO THIS WAIVER.



(l) Obligations of Investors. The Company acknowledges that the obligations of each
Investor under this Agreement are several and not joint with the obligations of any other Investor,
and no Investor shall be responsible in any way for the performance of the obligations of any other
Investor under this Agreement. The decision of each Investor to enter into to this Agreement has
been made by such Investor independently of any other Investor. The Company further acknowledges
that nothing contained in this Agreement, and no action taken by any Investor pursuant hereto,
shall be deemed to constitute the Investors as a partnership, an association, a joint venture or
any other kind of entity, or create a presumption that the Investors are in any way acting in
concert or as a group with respect to such obligations or the transactions contemplated hereby.
Each Investor shall be entitled to independently protect and enforce its rights, including without
limitation, the rights arising out of this Agreement, and it shall not be necessary for any other
Investor to be joined as an additional party in any proceeding for such purpose.



Each Investor has been represented by its own separate legal counsel in their review and
negotiation of this Agreement and with respect to the transactions contemplated hereby. The Company
has elected to provide all Investors with the same terms and Agreement for the convenience of the
Company and not because it was required or requested to do so by the Investors. The Company
acknowledges that such procedure with respect to this Agreement in no way creates a presumption
that the Investors are in any way acting in concert or as a group with respect to this Agreement or
the transactions contemplated hereby or thereby.



[Signature pages follow]




1




IN WITNESS WHEREOF, the parties have executed this Agreement or caused their duly
authorized officers to execute this Agreement as of the date first above written.



	 	 	 
	The Company:

	 	AVALON PHARMACEUTICALS, INC.
	 
	 	 
	
 
	 	By: /s/ Kenneth C. Carter
	
 
	 	 
	
 
	 	Name: Kenneth C. Carter

Title: President and Chief Executive Officer
	 
	 	 






2




	 	 	 
	 
	 	 
	The Investors:

	 	BIOTECHNOLOGY VALUE FUND, L.P.

By: BVF Partners, L.P., its general partner

By: BVF Inc., its general partner
	
 
	 	By: /s/ Mark N. Lampert
	
 
	 	 
	
 
	 	Mark N. Lampert, President
	 
	 	 






3




	 	 	 
	 
	 	 
	
 
	 	BIOTECHNOLOGY VALUE FUND II, L.P.

By: BVF Partners, L.P., its general partner

By: BVF Inc., its general partner
	
 
	 	By: /s/ Mark N. Lampert
	
 
	 	 
	
 
	 	Name: Mark N. Lampert

Title: President
	 
	 	 






4




	 	 	 
	 
	 	 
	
 
	 	BVF INVESTMENTS, L.L.C.

By: BVF Partners, L.P., its manager

By: BVF Inc, its general partner
	
 
	 	By: /s/ Mark N. Lampert
	
 
	 	 
	
 
	 	Name: Mark N. Lampert

Title: President
	 
	 	 






5




	 	 	 
	 
	 	 
	
 
	 	INVESTMENT 10, L.L.C.

By: BVF Partners, L.P., its attorney-in-fact

By: BVF Inc., its general partner
	
 
	 	By: /s/ Mark N. Lampert
	
 
	 	 
	
 
	 	Name: Mark N. Lampert

Title: President
	 
	 	 






6




	 	 	 
	 
	 	 
	
 
	 	XMARK JV INVESTMENT PARTNERS, LLC
	 
	 	 
	
 
	 	By: /s/ Michael D. Kaye
	
 
	 	 
	
 
	 	Name: Michael D. Kaye

Title: Chief Investment Officer
	 
	 	 






7




	 	 	 
	 
	 	 
	
 
	 	XMARK OPPORTUNITY FUND, L.P.
	 
	 	 
	
 
	 	By: /s/ Michael D. Kaye
	
 
	 	 
	
 
	 	Name: Michael D. Kaye

Title: Chief Investment Officer
	 
	 	 






8




	 	 	 
	 
	 	 
	
 
	 	XMARK OPPORTUNITY FUND, LTD.
	 
	 	 
	
 
	 	By: /s/ Michael D. Kaye
	
 
	 	 
	
 
	 	Name: Michael D. Kaye

Title: Chief Investment Officer






9




	 	 	 
	 	 	FORT MASON MASTER, LP	 
	 	 	By:	 	 	 	/s/	 	 	Dan German
	 	 	Name:	 	Dan German
	 	 	Title:	 	 	 	 	Managing Member
	 	 	FORT MASON PARTNERS, LP	 
	 	 	By:	 	 	 	/s/	 	 	Dan German
	 	 	 	 	 	Name:	Dan German	 
	 	 	 	 	 	Title:	 	 	 	Managing Member





10




Exhibit A




Plan of Distribution




The selling stockholders, which as used herein includes donees, pledgees, transferees or other
successors-in-interest selling shares of common stock or interests in shares of common stock
received after the date of this prospectus from a selling stockholder as a gift, pledge,
partnership distribution or other transfer, may, from time to time, sell, transfer or otherwise
dispose of any or all of their shares of common stock or interests in shares of common stock on any
stock exchange, market or trading facility on which the shares are traded or in private
transactions. These dispositions may be at fixed prices, at prevailing market prices at the time
of sale, at prices related to the prevailing market price, at varying prices determined at the time
of sale, or at negotiated prices.



The selling stockholders may use any one or more of the following methods when disposing of
shares or interests therein:



• ordinary brokerage transactions and transactions in which the broker-dealer solicits
purchasers;



• block trades in which the broker-dealer will attempt to sell the shares as agent, but may
position and resell a portion of the block as principal to facilitate the transaction;



• purchases by a broker-dealer as principal and resale by the broker-dealer for its account;



• an exchange distribution in accordance with the rules of the applicable exchange;



• privately negotiated transactions;



• short sales effected after the date the registration statement of which this Prospectus is a
part is declared effective by the SEC;



• through the writing or settlement of options or other hedging transactions, whether through
an options exchange or otherwise;



• broker-dealers may agree with the selling stockholders to sell a specified number of such
shares at a stipulated price per share; and



• a combination of any such methods of sale.



The selling stockholders may, from time to time, pledge or grant a security interest in some
or all of the shares of common stock owned by them and, if they default in the performance of their
secured obligations, the pledgees or secured parties may offer and sell the shares of common stock,
from time to time, under this prospectus, or under an amendment or supplement to this prospectus
under Rule 424(b)(3) or other applicable provision of the Securities Act amending the list of
selling stockholders to include the pledgee, transferee or other successors in interest as selling
stockholders under this prospectus. The selling stockholders also may transfer the shares of
common stock in other circumstances, in which case the transferees, pledgees or other successors in
interest will be the selling beneficial owners for purposes of this prospectus.



In connection with the sale of our common stock or interests therein, the selling stockholders
may enter into hedging transactions with broker-dealers or other financial institutions, which may
in turn engage in short sales of the common stock in the course of hedging the positions they
assume. The selling stockholders may also sell shares of our common stock short and deliver these
securities to close out their short positions, or loan or pledge the common stock to broker-dealers
that in turn may sell these securities. The selling stockholders may also enter into option or
other transactions with broker-dealers or other financial institutions or the creation of one or
more derivative securities which require the delivery to such broker-dealer or other financial
institution of shares offered by this prospectus, which shares such broker-dealer or other
financial institution may resell pursuant to this prospectus (as supplemented or amended to reflect
such transaction).



The aggregate proceeds to the selling stockholders from the sale of the common stock offered
by them will be the purchase price of the common stock less discounts or commissions, if any. Each
of the selling stockholders reserves the right to accept and, together with their agents from time
to time, to reject, in whole or in part, any proposed purchase of common stock to be made directly
or through agents. We will not receive any of the proceeds from this offering.



The selling stockholders also may resell all or a portion of the shares in open market
transactions in reliance upon Rule 144 under the Securities Act of 1933, provided that they meet
the criteria and conform to the requirements of that rule.



The selling stockholders and any underwriters, broker-dealers or agents that participate in
the sale of the common stock or interests therein may be “underwriters” within the meaning of
Section 2(11) of the Securities Act. Any discounts, commissions, concessions or profit they earn
on any resale of the shares may be underwriting discounts and commissions under the Securities Act.
Selling stockholders who are “underwriters” within the meaning of Section 2(11) of the Securities
Act will be subject to the prospectus delivery requirements of the Securities Act.



To the extent required, the shares of our common stock to be sold, the names of the selling
stockholders, the respective purchase prices and public offering prices, the names of any agents,
dealer or underwriter, any applicable commissions or discounts with respect to a particular offer
will be set forth in an accompanying prospectus supplement or, if appropriate, a post-effective
amendment to the registration statement that includes this prospectus.



In order to comply with the securities laws of some states, if applicable, the common stock
may be sold in these jurisdictions only through registered or licensed brokers or dealers. In
addition, in some states the common stock may not be sold unless it has been registered or
qualified for sale or an exemption from registration or qualification requirements is available and
is complied with.



We have advised the selling stockholders that the anti-manipulation rules of Regulation M
under the Exchange Act may apply to sales of shares in the market and to the activities of the
selling stockholders and their affiliates. In addition, we will make copies of this prospectus (as
it may be supplemented or amended from time to time) available to the selling stockholders for the
purpose of satisfying the prospectus delivery requirements of the Securities Act. The selling
stockholders may indemnify any broker-dealer that participates in transactions involving the sale
of the shares against certain liabilities, including liabilities arising under the Securities Act.



We have agreed to indemnify the selling stockholders against liabilities, including
liabilities under the Securities Act and state securities laws, relating to the registration of the
shares offered by this prospectus.



We have agreed with the selling stockholders to keep the registration statement of which this
prospectus constitutes a part effective until the earlier of (1) such time as all of the shares
covered by this prospectus have been disposed of pursuant to and in accordance with the
registration statement or (2) the date on which the shares may be sold pursuant to Rule 144(k) of
the Securities Act.




11