Exhibit 10.3
 
September 1, 2006  
Mr. Guy Macdonald
125B Magazine Street
Cambridge, MA 02139
 
     Re:      Renewal of Employment Term  
Dear Guy:
We are pleased to confirm the renewal of the term of your employment with the
Idenix Pharmaceuticals, Inc. (the “Company”) and to amend certain terms of the
Employment Agreement dated July 28, 2003 (the “Employment Agreement”) between
you and the Company.
Specifically, the first employment renewal term (the “First Renewal Term”) shall
be for a period of three (3) years. The First Renewal Term will commence on
September 2, 2006 and continue thereafter through September 1, 2009, unless
sooner terminated pursuant to the terms of the Employment Agreement. Upon
expiration of the First Renewal Term, each successive renewal period will be for
a term of one year and will automatically renew unless either party gives notice
to the other not less than 90 calendar days prior to the expiration of the then
current employment term. The Initial Term will continue through September 1,
2006.
We reaffirm that at the commencement of the First Renewal Term, your Base Salary
will continue to be $313,635 and the Target Bonus will continue to be 50%.
You acknowledge and agree that all payments due to you from the Company pursuant
to Section 3.G of the Employment Agreement, as previously modified, have been
paid to you and all obligations of the Company with respect thereto are fully
satisfied.
For purposes of notices contemplated by Section 11 of the Employment Agreement,
you are hereby advised that all notices and correspondence to the Company should
be sent to the address set forth above to the attention of the Company’s Chief
Executive Officer with a copy (which shall not constitute notice) to the
Company’s Vice President, Human Resources.
Capitalized terms used but not defined herein shall have the meaning ascribed to
such terms in the Employment Agreement. Except as modified hereby, the terms of
the Employment Agreement shall remain in full force and effect.
If the terms above reflect our agreement, please acknowledge such by signing in
the space provided below and returning one acknowledged copy of this letter to
me.
 
Very truly yours,

                  /s/ Jean-Pierre Sommadossi       Jean-Pierre Sommadossi     
Chairman and Chief Executive Officer     

Acknowledged and agreed this 1st day of
September 2006.

                  By:   /s/ Guy Macdonald         Guy Macdonald             

cc: Mr. Paul Fanning