Exhibit 10.9B
AMENDMENT NO.1
TO
AMENDED AND RESTATED EMPLOYMENT AGREEMENT
     This Amendment No. 1 to Amended and Restated Employment Agreement is made
as of this ___ 26th___ day of December, 2006 (this “Amendment”), between AVALON
PHARMACEUTICALS, INC., a Delaware corporation (“Company”) and DAVID BOL
(“Executive”).
     Company and Executive are each sometimes referred to as a “Party,” and are
sometimes referred to together as the “Parties.”
Background:
     The Parties entered into an Amended and Restated Employment Agreement on
April 21, 2005 (the “Employment Agreement”).
     In consideration of Executive’s continued employment with Company, the
Parties want to amend the Employment Agreement on the terms and conditions set
forth in this Amendment.
     Now, therefore, in consideration of the foregoing, the Parties agree as
follows:
     1. Capitalized terms used in this Amendment without definition, shall have
the meanings give those terms in the Employment Agreement.
     2. The first paragraph under the caption “Termination” of the Employment
Agreement is amended to read in its entirety as follows:
“Upon termination for any reason, the Company shall pay you within two weeks of
such termination, your current base salary earned through the termination date,
plus accrued vacation, if any, and other benefits or payments, if any, to which
you are entitled as provided in accordance with the terms and conditions of such
benefit plan. In the event you are terminated by the Company without “Cause” (as
hereinafter defined), or if you terminate your employment with the Company for
“Good Reason” (as hereinafter defined), the Company shall (i) pay you a lump sum
severance payment equal to six months of your base salary as in effect at the
time of termination (nine months in the event such termination is without Cause
or for Good Reason within eighteen months after a Change in Control (as
hereinafter defined)); (ii) provide you with outplacement services; and
(iiii) reimburse you for premiums you pay for health care insurance under the
Consolidated Omnibus Budget Reconciliation Act (“COBRA”), for the same level of
coverage that you maintain at the time of your termination, for a period up to
six months (nine months in the event such termination is without Cause or for
Good Reason within eighteen months after a Change in Control) following
termination, provided you elect COBRA coverage. The Company’s

 

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reimbursement obligation will end immediately if you become eligible to obtain
health care insurance from any other employer during the payment period. You
shall not be required to mitigate damages by seeking employment elsewhere. If
you are terminated with Cause, the Company shall pay you only your current base
salary earned through the termination date, plus accrued vacation, if any, to
which you are entitled as provided in accordance with the terms and conditions
of such benefit plan.”
     3. A new paragraph shall be added under the caption “Termination” of the
Employment Agreement at the end of such section and shall read in its entirety
as follows:
“Should the Company be the subject of a Change in Control, the Company shall
immediately vest one-half (1/2) of all shares and options granted to you that
have not vested as of the date the Change in Control takes effect.”
     4. Except as set forth in this Amendment, the terms and conditions of the
Employment Agreement shall remain in full force and effect.
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     IN WITNESS WHEREOF, the Parties have executed this Amendment to Amended and
Restated Employment Agreement as of the date first set forth above.

            AVALON PHARMACEUTICALS, INC.
      By:  /s/ Kenneth C. Carter       Name:       Title: CEO and President     
  EXECUTIVE:
      /s/ David K. Bol       David Bol           

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