Exhibit 10.1
AMENDMENT NO. 1
TO
TERM NOTE
     This AMENDMENT NO. 1 (this “Amendment”) to the Term Note dated October 27,
2008, in the original principal amount of Three Million Dollars ($3,000,000)
payable to the order of Clinical Data, Inc. (“CLDA,” and such Term Note referred
to as the “Term Note”) is made as of this 12th day of January, 2009 by and
between Avalon Pharmaceuticals, Inc. (“Avalon”) and CLDA.
     WHEREAS, Avalon and CLDA desire to amend the Term Note to extend the
Maturity Date, as that term is defined in Section 4 of the Term Note, from
March 31, 2009 to April 30, 2009.
     NOW, THEREFORE, in consideration of the mutual covenants and agreements set
forth herein, in the Term Note and in the Note Purchase Agreement, as that term
is defined in Section 1 of the Term Note, and for other good and valuable
consideration, the receipt and adequacy of which is hereby acknowledged, the
parties hereto agree as follows:
     SECTION 1. Amendment to the Term Note.
     Section 4 of the Term Note is hereby amended by deleting it in its entirety
and replacing it with the following:
Maturity Date. All of the amounts due hereunder shall be due and payable on the
earlier to occur of April 30, 2009, or such earlier date as such maturity may be
accelerated pursuant to the terms hereof (the “Maturity Date”).
     SECTION 2. Full Force and Effect. The Term Note shall remain in full force
and effect, except as modified hereby.
     SECTION 3. Counterparts. This Amendment may be executed by one or more of
the parties hereto on any number of separate counterparts, and all of said
counterparts taken together shall be deemed to constitute one and the same
instrument.
     SECTION 4. Governing Law. This Amendment shall be construed in accordance
with and governed by the laws of the State of New York, without regard to its
principles of conflicts of laws.
     SECTION 5. Effectiveness. This Amendment shall become effective upon the
execution and delivery hereof by Avalon and CLDA.
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          IN WITNESS WHEREOF, the parties hereto have caused this Amendment to
be executed and delivered as of the date first above written.

                  Clinical Data, Inc.    
 
           
 
  By:   /s/ Caesar J. Belbel    
 
           
 
  Name:   Caesar J. Belbel    
 
  Title:   Executive Vice President,    
 
      Chief Legal Officer and Secretary    
 
                Avalon Pharmaceuticals, Inc.    
 
           
 
  By:   /s/ Kenneth C. Carter    
 
           
 
  Name:   Kenneth C. Carter    
 
  Title:   President & Chief Executive Officer