Exhibit
10.1


May
16, 2007


John Batty


Address


Dear
John,


It is our pleasure to offer you the position of Chief
Financial Officer and Executive Vice President as a Section 16(b) Officer with
Affymetrix at an annual salary of $360,000 (bi-weekly $13,846.15) reporting
to Steve Fodor, Chief Executive Officer.


You will be eligible to participate in the Affymetrix
Annual Bonus Program with an award level targeted at 50% of annual base salary.
The actual bonus amount is determined each year by the Compensation Committee
of the Board of Directors based on corporate achievement — financial
performance and corporate goals — and your individual goal achievement. In your
first year of employment, this bonus will be pro-rated based on your
start date. For 2007 only, your minimum bonus will be the pro-rated amount of
your target bonus so long as you remain employed with Affymetrix on the day the
bonus is paid in February of 2008.


In addition, we will recommend to the Compensation
Committee of the Board of Directors of Affymetrix that you be granted two
equity awards. The first is a Stock Option Grant of 30,000 shares of common
stock of Affymetrix. These options will vest 25% per year over a four (4) year
period beginning on your start date, and will have an exercise price equal to
fair market value on the grant date. If you are involuntarily terminated
without Cause (as defined in the Company’s Amended and Restated 2000 Equity
Incentive Plan), you will have 12 months after termination to exercise these
options to the extent they are vested on your termination date, but in no event
may the options be exercised after the original expiration date of the option. This
is subject to you signing a general release of claims.


The second is a grant of 30,000 full-value restricted
shares of common stock of Affymetrix, of which 10,000 will vest on the first
anniversary of your start date, 10,000 will vest on the second anniversary of your
start date, and 5,000 will vest on each of the third and fourth anniversaries
of your start date, provided that you continue to be an employee of Affymetrix
on such dates. If you are involuntarily terminated without Cause (as defined in
the Company’s Amended and Restated 2000 Equity Incentive Plan) after the third
anniversary of your start date but prior to your final vesting date, the
remaining unvested portion of this restricted share











award will become vested. This is subject to you
signing a general release of claims. The terms of these grants will be governed
in all respects by the
terms of the applicable Affymetrix equity incentive plan and the equity
agreement that will be provided to you after commencement of your employment.


As a condition of employment, we will require that you
sign a copy of the company’s Confidentiality and Nondisclosure Agreement.


Federal Immigration Law requires that all employers
verify each individual’s eligibility to work in the United States, including
U.S. citizens. Your employment offer is contingent upon your providing satisfactory
proof of identity and authorization to work in the United States. Please bring
the appropriate original documentation on your first day of work. A list of
acceptable I-9 documentation is attached for your review.


Your employment is at will, and no special or implied
conditions of employment are established unless they are made in writing by the
CEO of Affymetrix.


This offer is contingent upon satisfactory completion
of reference check and background checks.


If you have any questions, please feel free to contact
me at (408) 731-5622. To indicate acceptance of
this offer, please return a signed copy of this letter to me by May 16, 2007, close
of business. You can fax the letter back to me at (408) 731-5855.


John, your skills, experience and high potential
are respected and valued by everyone with whom you met here at Affymetrix. We
look forward to having you accept this offer and join us in strengthening our Finance
Department and realize the promise of our technology to enhance the quality of
life.


Sincerely,


/s/
Lori Ciano


Lori
Ciano


Senior Vice President, Human Resources


Offer
Acceptance:


	
  /s/ John Batty

  	
   

  	
  05/16/2007

  
	
  John Batty

  	
   

  	
  Date

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  06/18/2007

  	
   

  	
   

  
	
  Start Date