Exhibit 10.1

AMENDMENT NO. 2 TO

EMPLOYMENT AGREEMENT

THIS AMENDMENT NO. 2 TO EMPLOYMENT AGREEMENT (the “Amendment”) made as of
May 10, 2006 (“Effective Date”) by and between BioMarin Pharmaceutical Inc., a
Delaware corporation (the “Company”) and Jean-Jacques Bienaimé (“Employee”).

 

1. This Amendment is intended to amend and modify that certain Employment
Agreement by and between the Company and Employee dated May 11, 2005 as
previously amended December 15, 2005 (the “Agreement”). The Agreement, together
with this Amendment, shall constitute a single agreement. Capitalized terms not
otherwise defined in this Amendment shall have the meaning ascribed to such
terms in the Agreement. Except as expressly modified by this Amendment, the
Agreement shall remaining full force and effect according to its terms.

 

2. Effective May 11, 2006, Employee’s Base Salary shall be increased to
$607,760. per annum. The Base Salary shall be reviewed on the same schedule as
is applicable to other Company executives and may be increased by action of the
Board or appropriate Committee of the Board.

 

3. Effective on May 11, 2006, Employee shall be granted options to purchase
250,000 shares of Common Stock under the Company’s 1997 Stock Plan with an
exercise price equal to the closing price per share of Common Stock as reported
by Nasdaq on May 11, 2006 and will have the same vesting schedule typically used
for grants to all Company executives and employees, namely, 4-year vesting with
monthly vesting following an initial 6-month cliff. Such options shall be in
lieu of the options to otherwise be granted to Employee for 2006 pursuant to
Section 4(c)(ii) of the Agreement. The grant date for future options pursuant to
Section 4(c)(ii) shall be the same date as options are generally granted to
other BioMarin executives, provided that if no options are generally granted to
BioMarin executives during any consecutive 5 month period between December and
April, the grant date for Employee’s options shall continue to be May 11 of such
respective year of employment.

 

4. The Agreement, as amended by this Amendment contains the sole and entire
agreement of the parties and supersedes all prior agreements and understandings
between the Employee and the Company and cannot be modified or changed by any
oral or verbal promise or statement by whomsoever made; nor shall any written
modification of it be binding upon the Company until such written modification
shall have been approved in writing by the Board.

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5. This Agreement may be executed and delivered (including by facsimile
transmission) in one or more counterparts, each of which shall be deemed an
original, but all of which together shall constitute one and the same
instrument.

IN WITNESS WHEREOF, the parties to this Amendment have executed this Amendment
as of the date first written above.

 

BIOMARIN PHARMACEUTICAL INC.     EMPLOYEE By:   /s/ Pierre Lapalme    

By:

  /s/ Jean-Jacques Bienaimé Name:   Pierre Lapalme     Name:   Jean-Jacques
Bienaimé Its:   Chairman of the Board of Directors