Exhibit
      10.1

    


    


    July
      27,
      2007

     

    Thane
      Kreiner

    c/o
      Affymetrix, Inc.

    3420
      Central Expressway

    Santa
      Clara, CA 95051

    


    Dear
      Thane:

     

    This
      letter agreement (the “Agreement”) sets forth our mutual
      agreement with respect to your separation from employment with Affymetrix,
      Inc.
      (the “Company”).

     

    1.        Separation
      Date.  Effective July 27, 2007 (the “Separation
      Date”), your employment with the Company (including any position you
      hold with any of the Company’s subsidiaries) has terminated.

     

    2.        Separation
      Benefits.  Subject to your signing and letting become effective
      the release set forth in Section 3 below and continued compliance with the
      covenants set forth in the Confidentiality Agreement (as defined below) and
      Section 4 of this Agreement, you will receive the following:

     

    (a)                 An
      amount equal to (i) $362,308, representing the salary you would have received
      through October 20, 2008, plus (ii) $117,000, representing a portion of your
      annual target bonus, each of which shall be paid in six equal installments
      over
      the six-month period following the Separation Date.  The first payment
      shall be made within ten days following the execution this
      Agreement.

     

    (b)                 To
      the extent you elect health coverage pursuant to COBRA, Company reimbursement
      of
      your COBRA premiums through the earlier of (i) October 20, 2008 or (ii) the
      date
      on which you become eligible for group coverage with another
      employer.

     

    (c)                 Accelerated
      vesting of your stock options and restricted stock to the extent they would
      have
      vested if you had remained employed through October 20, 2008.  Your
      vested stock options shall remain exercisable until the earlier of
      (i) January 20, 2009 (ii) the maximum term set forth in the applicable
      stock option or restricted stock agreements or (iii) termination of all
      stock options and or restricted stock in accordance with the terms of the
      applicable stock plans; provided that you understand that any stock
      options with an exercise period longer than three months following the
      Separation Date shall not be considered “incentive stock options”.

     

    (d)                 The
      Company will pay for up to 12 months of a job placement service in an aggregate
      amount not to exceed $20,000.

     

    
      
        
        

      

      
        
        

        
          

        

      

      
        
        

      

    

     

    (e)                 The
      Company will pay for reasonable legal counsel fees incurred by you in connection
      with the execution of this Agreement.  You will provide the Company
      with reasonable evidence of such fees in the form of a summary bill prior to
      receiving reimbursement.  The amount reimbursed by the Company
      pursuant to this clause (e) will not exceed $50,000.

     

    Notwithstanding
      anything in this Agreement to the contrary, to the extent that the Company
      determines in good faith that any payment provided for in this Agreement
      constitutes a “deferral of compensation” under Section 409A of the Internal
      Revenue Code, then such payment shall not be paid prior to the earlier of:
      (i) the date that is six months following the Separation Date or
      (ii) your death.

     

    3.        Release.

     

    (a)                 You
      acknowledge that the following releases shall extend to unknown, as well as
      known claims, and hereby waive the application of any provision of law,
      including, without limitation, Section 1542 of the California Civil Code,
      that purports to limit the scope of a general
      release.  Section 1542 of the California Civil Code
      provides:

     

    “A
      GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW
      OR
      SUSPECT TO EXIST IN HIS FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH IF
      KNOWN BY HIM MUST HAVE MATERIALLY AFFECTED HIS SETTLEMENT WITH THE
      DEBTOR.”

     

    (b)                 You
      agree to and do fully and completely release, discharge and waive any and all
      claims, complaints, causes of action or demands of whatever kind which you
      have
      or may have against the Company, its subsidiaries, affiliates, predecessors
      and
      successors and all its directors, officers, employees, stockholders and other
      investors by reason of any event, matter, cause or thing which has occurred
      prior to the date hereof (“Executive Claims”).  You
      understand and accept that this release specifically covers, but is not limited
      to, any and all Executive Claims relating in any way to compensation, to any
      previous agreements between you and the Company related to your employment,
      or
      to any other terms, conditions or circumstances of your employment with the
      Company or the termination thereof, whether for severance or based on statutory
      or common law claims for employment discrimination (including discrimination
      on
      the basis of sex, age, religion or disability, including specifically any claims
      under the Age Discrimination in Employment Act (the “ADEA”),
      Title VII of the Civil Rights Act of 1964, as amended, or the Americans with
      Disabilities Act of 1990), wrongful discharge, breach of contract or any other
      theory, whether legal or equitable.  Notwithstanding the foregoing,
      you do not waive any rights to which you may be entitled to seek to enforce
      this
      Agreement, or to seek indemnification with respect to liability incurred by
      you
      as an employee, officer or director of the Company in accordance with the
      Company’s bylaws and any indemnification agreement between you and the Company
      (the “Indemnification Agreement”).

     

    (c)                 Acknowledgement
      of Waiver of Claims Under ADEA.  You acknowledge that you are
      waiving and releasing any rights you may have under the ADEA and that
      this

     

    
      
        
        

      

      
        
        

        
          

        

      

      
        
        

      

    

     

    waiver
      and
      release is knowing and voluntary.  You and the Company agree that this
      waiver and release does not apply to any rights or claims that may arise under
      ADEA after the Separation Date.  You acknowledge that the
      consideration given for this waiver and release is in addition to anything
      of
      value to which you were already entitled.  You further acknowledge
      that you have been advised by this writing that:

     

    (i)              You
      should consult with an attorney prior to executing this
      Agreement.

     

    (ii)              You
      have up to 21 days within which to consider this Agreement.

     

    (iii)              You
      have seven days following your execution of this Agreement to revoke the release
      set forth in this Section, in which case the Company shall have no obligations
      to you under this Agreement.

     

    4.        Restrictive
      Covenants.

     

    (a)                 Confidentiality
      Agreement.  Your obligations under your existing Confidentiality
      and Invention Agreement with the Company (the “Confidentiality
      Agreement”) remain in effect after the effective date of this
      Agreement.

     

    (b)                 Non-Solicitation.  Without
      limiting the foregoing, you agree that through the date that is 12 months
      following the Separation Date: (i) you will not directly or indirectly
      solicit any employee of the Company or any of its affiliates to terminate his
      or
      her employment with the Company or any of its affiliates; and (ii) you will
      not directly or indirectly solicit customers or suppliers of the Company based
      on confidential information of the Company or solicit any such person to
      terminate his, her or its relationships with the Company.

     

    (c)                 No
      Disparagement.  During and after your employment with the
      Company, you agree that you shall not make negative statements or
      representations, or otherwise communicate negatively, directly or indirectly,
      in
      writing, orally, or otherwise, or take any action which may, directly or
      indirectly, disparage or be damaging to the Company, its subsidiaries,
      affiliates, successors or their officers, directors, employees, business or
      reputation, except as may be required by law or by any regulatory
      authority.  The Company agrees that neither it nor its officers and
      directors shall make any negative statements or representations, or otherwise
      communicate negatively, directly or indirectly, in writing, orally or otherwise,
      or take any action which may, directly or indirectly, disparage or be damaging
      to you or your reputation.

     

    (d)                 Employment.  As
      specific consideration for a portion of the severance payments and benefits
      provided under Section 2 of this Agreement, you agree not to work for either
      Agilent or Illumina (or their affiliates or successors) for a period of 12
      months after the Separation Date.  In the event of your breach of this
      clause (d), the Company shall have the right to cease any payments and benefits
      being provided to you pursuant to Section 1 of this Agreement.

     

    
      
         

      

      
         

        
          

        

      

      
         

      

    

     

    (e)                 Remedies.  You
      and the Company acknowledge and agree that the Parties’ remedies at law for a
      breach or threatened breach of any of the provisions of this Section would
      be
      inadequate and, in recognition of this fact, you agree that, in the event of
      a
      breach or threatened breach, in addition to any remedies at law, the Parties,
      without posting any bond, shall be entitled to obtain equitable relief in the
      form of specific performance, temporary restraining order, temporary or
      permanent injunction or any other equitable remedy which may then be
      available.

     

    5.        Entire
      Agreement; Amendment.  Except as expressly set forth herein, and
      except for your stock option agreements (as amended hereby), the Confidentiality
      Agreement and the Indemnification Agreement, this Agreement shall supersede
      any
      and all existing agreements between you and the Company or any of its affiliates
      relating to the terms of your employment and contains the entire understanding
      of the parties with respect to your employment and the termination
      thereof.  This Agreement may not be altered, modified or amended
      except by a written agreement signed by both parties hereto.

     

    6.        No
      Waiver.  The failure of a party to insist upon strict adherence
      to any term of this Agreement on any occasion shall not be considered a waiver
      of such party’s rights or deprive such party of the right thereafter to insist
      upon strict adherence to that term or any other term of this
      Agreement.

     

    7.        Severability.  In
      the event that any one or more of the provisions of this Agreement shall be
      or
      become invalid, illegal or unenforceable in any respect, the validity, legality
      or enforceability of the remaining provisions of this Agreement shall not be
      affected thereby.

     

    8.        Assignment.  This
      Agreement shall inure to the benefit of and be binding upon the parties hereto
      and their respective heirs, representatives, successors and
      assigns.  This Agreement shall not be assignable by you and shall be
      assignable by the Company only to an affiliate or successor thereof, which
      affiliate or successor shall assume all of the Company’s obligations to you
      hereunder.

     

    9.        Acknowledgement.  You
      acknowledge that you have carefully read this Agreement, fully understand and
      accept all of its provisions and sign it voluntarily of your own free
      will.

     

    10.      Withholding.  You
      agree that any payments to which you may be entitled pursuant to this Agreement
      are subject to withholding by the Company of any applicable federal, state
      or
      local taxes; provided that you understand that you remain ultimately
      responsible for any tax consequences hereunder.

     

    11.      Governing
      Law.  This Agreement shall be governed by and construed in
      accordance with the laws of the State of California, without regard for the
      conflicts of law principles thereof.

     

    12.      Arbitration.

     

    (a)                 
      Any dispute or controversy arising out of, relating to, or in connection with
      this Agreement, or the interpretation, validity, construction, performance,
      breach, or termination thereof, shall be settled by binding and confidential
      arbitration to be held in Santa Clara County, California, in accordance with
      the
      National Rules for the Resolution of Employment Disputes then

     

    
      
         

      

      
         

        
          

        

      

      
         

      

    

     

    in
      effect
      of the American Arbitration Association (the
“Rules”).  The arbitrator may grant injunctions or
      other relief in such dispute or controversy.  The decision of the
      arbitrator shall be final, conclusive and binding on the parties to the
      arbitration.  Judgment may be entered on the arbitrator's decision in
      any court having jurisdiction.

     

    (b)                 The
      arbitrator(s) shall apply California law to the merits of any dispute or claim,
      without reference to conflicts of law rules.  The arbitration
      proceedings shall be governed by federal arbitration law and by the Rules,
      without reference to state arbitration law.  You hereby consent to the
      personal jurisdiction of the state and federal courts located in California
      for
      any action or proceeding arising from or relating to this Agreement or relating
      to any arbitration in which the parties are participants.

     

    (c)           The
      Company and you shall each pay one-half of the costs and expenses of the
      arbitration, and each party shall bear its own respective attorneys’ fees and
      all other costs, unless otherwise required or allowed by law and awarded by
      the
      arbitrator.

     

    13.                   Notices.
      Except as otherwise explicitly provided in this Agreement, any notice provided
      hereunder will be deemed to be given when delivered in writing by hand, by
      facsimile or sent by overnight courier.  All notices to the Company
      will be marked confidential and addressed to the Company’s General
      Counsel.  All notices to you will be addressed to your most recent
      address as reflected on the Company’s payroll and sent to such other address as
      you may provide from time to time by notice to the Company, or any other
      persons or
      addresses as you may request from time to time by notice to the
      Company.

     

    14.                   Counterparts.  This
      Agreement may be signed in counterparts, each of which shall be an original,
      with the same effect as if the signatures thereto and hereto were upon the
      same
      instrument.

     

     

     

     

     

    
      
         

      

      
         

        
          

        

      

      
         

      

    

     

    Please
      acknowledge your acceptance of the foregoing by signing where indicated
      below.

     

    
      	 	
              AFFYMETRIX,
                INC.

            	 
	 	 	 	 
	 	 	 	 
	 	
              By:

            	
              /s/
                Barbara A. Caulfield

            	 
	 	
              Name:
                Barbara A. Caulfield

            	 
	 	
              Title:   
                EVP and General Counsel

            	 


    

    


    Accepted
      and Agreed:

     

    /s/
      Thane Kreiner

    Thane
      Kreiner

     

    July
      27, 2007

    Date