Document:

Employment Agreement between the Registrant and Daniel Clutter

 Exhibit 10.21 
 NimbleGen Systems, Inc. 
 One Science Ct. 
 Madison, WI 53711 
 January 5, 2004 
 Mr. Daniel Clutter 
 946 Lewis Place 
 Geneva, IL 60134 
 Dear Dan: 
 This letter will confirm our agreement with respect to the terms of your employment by NimbleGen Systems Inc. (the “Company”). We have agreed as
follows: 
 1. Terms of Employment and Duties. You will be employed by the Company as Director of Sales starting on January 1,
2004. The terms of this letter, if not earlier accepted, will expire January 8, 2004 at 5:00P.M. During the term of your employment, you agree to devote your best efforts and all of your business time, attention and skill to the business and
affairs of the Company as required by its business needs. 
 2. Compensation. 
 (a) Base Salary. During the term of your employment, the Company will pay you a salary at the rate of $110,000 per annum, payable according to the
regular payroll practices of the Company. 
 (b) Commission. During the first year of your employment, and annually thereafter as
determined by the Board of Directors, you will be eligible to receive a commission based upon the Commission Program described in Exhibit A attached hereto and made part hereof. 
 (c) Withholding and Other Taxes. The Company will deduct from the payments to be made to you under this agreement any Federal, State or local
withholding or other taxes or charges which the Company is from time to time required to deduct under applicable law, and all amounts payable to you under this agreement are stated before any such deduction. 
 (d) Stock Options: As a key member of the NimbleGen team, you will be entitled to participate in the Company’s Incentive Stock Option Plan
which is administered by the Company’s Board of Directors. You will initially receive an option to purchase Fifty Thousand (50,000) shares of NimbleGen common stock. The specific terms of this option are delineated in the Stock Option
Agreement and in the Plan Document. These options will vest in 4 phases: 25% on each of the first four anniversaries of your first day of employment. In addition, based on your ability to increase the value of the Company, the Board of Directors may
be in a position to authorize the issuance of additional stock options. The intent here is to give you the opportunity to work with us to build a highly successful company and give you the opportunity to own potentially highly valuable stock.

 3. Expenses and Benefits. 
 (a) Expenses. The Company will pay or reimburse you for all reasonable automobile, travel, entertainment and like expenses ordinarily and
necessarily incurred by you in furtherance of the Company’s business. You will be required to submit an itemized account of such expenditures and such proof as may be necessary (in accordance with the Company’s policy and IRS regulations)
to establish to the satisfaction of the Company that such expenses were ordinary and necessary expenses incurred by you in furtherance of the business of the Company. Additionally, the Company will reimburse you reasonable hotel costs while staying
in the Madison, Wisconsin area. 
 (b) Fringe Benefits. During the term of your employment, you will be entitled to participate in any
vacation, health insurance, disability insurance, retirement, and other similar fringe benefit plans of the kinds and in the amounts now or at any time during such term provided generally to other exempt employees of the Company. You acknowledge
that you have no rights in any such plans except as expressly provided under the terms of such plans and that such plans may be terminated, modified or supplemented at any time. You also will be entitled to vacations during the term of your
employment in accordance with the Company’s policies as in effect from time to time for other exempt employees of the Company. Copies of any plans or other documents describing these benefits will be provided to you upon request. 
 4. Employment, Confidential Information, Invention Assignment, and Arbitration Agreement: As consideration for your employment at NimbleGen, you
will be required to sign the Company’s Employment, Confidential Information, Invention Assignment and Arbitration Agreement. A copy of this agreement is enclosed for your signature. Please contact me if you have any questions. 
 5. Indemnification. The Company agrees to indemnify you and hold you harmless from and against any loss, cost, expense or other damage (including
without limitation reasonable attorneys’ fees) suffered by you resulting from, arising out of or incurred with respect to any claim of patent infringement which arises out of your consulting services for or employment with the Company.

 6. Termination. Your employment by the Company is at will and may be terminated at any time by you, with 14 days prior written
notice, or by the Company. Nothing contained in this letter, the Employment, Confidential Information, Invention Assignment, and Arbitration Agreement, or the Stock Purchase Agreement will be construed as conferring upon you any right to remain
employed by the Company or affect the right of the Company to terminate your employment at any time. Upon your termination of employment, the Company will pay to you your salary through your date of termination and such other benefits in which you
are vested or 

  

			
	Phone: 608-218-7600	  	info@nimblegen.com
	FAX: 608-218-7601	  	www.nimblegen.com

 
are otherwise entitled through the date of your termination. Except as expressly provided above, the Stock Purchase Agreement or by law, the Company will
have no further obligations to you following your termination of employment. 
 7. Miscellaneous. 
 (a) This agreement will be binding on the Company and its successors and will insure to the benefit of and be enforceable by your personal or legal
representatives, heirs and successors. 
 (b) This agreement and all questions of its interpretation, performance and enforcement and the
rights and remedies of parties will be determined in accordance with the laws of the State of Wisconsin without application of conflict of law principles. 
 (c) This agreement supersedes any and all prior agreements, whether written or oral, between the Company or any representative thereof and you relating to the services performed by you for the Company or your
compensation for such services, and all such prior agreements are null and void. 
 (d) Any notice required or permitted to be given under
this agreement will be in writing and will be deemed given by: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next
business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next
day delivery, with written verification of receipt at the following addresses or to such other addresses either party shall specify by like notice: 
 if to the Company: 
 President and Chief Executive Officer 
 NimbleGen Systems Inc. 
 1 Science Court 
 Madison, WI 53711 
 with a copy to: 
 Kenneth C.
Hunt Esq. 
 Godfrey & Kahn, S.C. 
 780 North Water Street 
 Milwaukee, Wisconsin 53202 
 and if to you: 
 Mr. Daniel Clutter 
 946 Lewis Place 
 Geneva, IL 60134 
  

			
	Phone: 608-218-7600	  	info@nimblegen.com
	FAX: 608-218-7601	  	www.nimblegen.com

 (e) The Agreement may be amended or modified only upon the written consent of the Company and you.

 (f) You hereby represent and warrant to the Company that (a) neither the execution of this Agreement by you nor the performance of
any of your obligations or duties hereunder will conflict with or violate or constitute a breach of the terms of any employment or other agreement to which you are a party or by which you are bound, and (b) you are not required to obtain the
consent of any person, firm, corporation or other entity in order to enter into this Agreement or to perform any of your obligations or duties hereunder. 
 If this letter correctly sets forth your understanding of our agreement, please sign a copy in the space provided below and return it to the Company, together with an executed copy of the Employment, Confidential
Information, Invention Assignment, and Arbitration Agreement. 
  

	
	Very truly yours,
	
	NIMBLEGEN SYSTEMS INC.
	
	/s/ Thomas Palay
	 Thomas Palay
 Vice Chairman

  

	
	 I confirm my agreement with
 the terms and conditions of
letter.

	
	/s/ Daniel Clutter
	Date: January 7, 2004

  

			
	Phone: 608-218-7600	  	info@nimblegen.com
	FAX: 608-218-7601	  	www.nimblegen.com

 EXHIBIT A 
 COMMISSION PROGRAM 
 Pursuant to the Commission Program, NimbleGen will pay Sales Commissions to you at a Sales
Commission Rate as indicated in the Calendar Metrics indicated below on sales of products and services in excess of the Threshold, during the calendar year (“Eligible Sales”). Net Sales are the amount of Eligible Sales excluding sales
discount, shipping charges and sales tax, made in excess of the Threshold. Net Sales do not include revenues from sources other than for the sales of products and services and excludes, inter alia, grants from the United States Government and
Agencies thereof. It does not include revenues of the Company’s subsidiaries. 
 Commission is payable in the quarter subsequent to year-end. Commission
is paid only on Net Sales that are shipped and for which the Company has received payment. Products returned or rejected by the customer are credited in the quarter the return or rejection occurs. The Company is the final authority on what
constitutes Net Sales. The Company will evauate this Commission program after the initial year and may modify, change or eliminate the program. 
 Calendar 2004 Metrics 
  

			
	Threshold $10,000,000	  	
	Sales Commission Rate	  	
	 First $1,000,000 of Net Sales
	  	... One Percent
	 Sales in excess of the first $1,000,000 of Net Sales
	  	... Two Percent

  

			
	Phone: 608-218-7600	  	info@nimblegen.com
	FAX: 608-218-7601	  	www.nimblegen.comEmployment Agreement between the Registrant and Steven W. Smith

 Exhibit 10.22 
 NimbleGen Systems, Inc. 
 One Science Ct. 
 Madison, WI 53711 
 September 26, 2001 
 Mr. Steven W. Smith 
 2854 Richardson Street 
 Fitchburg, WI 53711 
 Dear Mr. Smith: 
 This letter will confirm our agreement with respect to the terms of your employment by NimbleGen Systems Inc. (the “Company”). We have agreed as
follows: 
 1. Terms of Employment and Duties. You will be employed by the Company as Vice President, Bioinformatics, starting on
November 25, 2001. The terms of this letter, if not earlier accepted, will expire September 26, 2001. During the term of your employment, you agree to devote your best efforts and all of your business time, attention and skill to the
business and affairs of the Company as required by its business needs. 
 2. Compensation. 
 (a) Base Salary. During the term of your employment, the Company will pay you a salary at the rate of $140,000.00 per annum, payable according to
the regular payroll practices of the Company. 
 (b) Withholding and Other Taxes. The Company will deduct from the payments to be made
to you under this agreement any Federal, State or local withholding or other taxes or charges which the Company is from time to time required to deduct under applicable law, and all amounts payable to you under this agreement are stated before any
such deduction. 
 (c) Stock Options: As a key member of the NimbleGen team, you will be entitled to participate in the Company’s
Incentive Stock Option Plan which is administered by the Company’s Board of Directors. You will receive initially an option to purchase Thirty Thousand (30,000) shares of NimbleGen common stock. The specific terms of this option are
delineated in the Stock Option Agreement and in the Plan Document. These options will vest in 4 phases: 25% on each of the first four anniversaries of your first day of employment. In addition, based on your ability to increase the value of the
Company, the Board of Directors may be in a position to authorize the issuance of additional stock options. The intent here is to give you the opportunity to work with us to build a highly successful company and give you the opportunity to own
potentially highly valuable stock. 

 3. Expenses and Benefits. 
 (a) Expenses. The Company will pay or reimburse you for all reasonable automobile, travel, entertainment and like expenses ordinarily and
necessarily incurred by you in furtherance of the Company’s business. You will be required to submit an itemized account of such expenditures and such proof as may be necessary (in accordance with the Company’s policy and IRS regulations)
to establish to the satisfaction of the Company that such expenses were ordinary and necessary expenses incurred by you in furtherance of the business of the Company. 
 (b) Fringe Benefits. During the term of your employment, you will be entitled to participate in any vacation, health insurance, disability insurance, retirement, and other similar fringe benefit plans of the
kinds and in the amounts now or at any time during such term provided generally to other executive officers of the Company. You acknowledge that you have no rights in any such plans except as expressly provided under the terms of such plans and that
such plans may be terminated, modified or supplemented at any time. You also will be entitled to vacations during the term of your employment in accordance with the Company’s policies as in effect from time to time for senior executives of the
Company. Copies of any plans or other documents describing these benefits will be provided to you upon request. 
 4. Employment,
Confidential Information, Invention Assignment, and Arbitration Agreement: As consideration for your employment at NimbleGen, you will be required to sign the Company’s Employment, Confidential Information, Invention Assignment and
Arbitration Agreement. A copy of this agreement is enclosed for your signature. Please contact me if you have any questions. 
 5.
Indemnification. The Company agrees to indemnify you and hold you harmless from and against any loss, cost, expense or other damage (including without limitation reasonable attorneys’ fees) suffered by you resulting from, arising out of
or incurred with respect to any claim of patent infringement which arises out of your consulting services for or employment with the Company. 
 6. Termination. Your employment by the Company is at will and may be terminated at any time by you, with 14 days prior written notice, or by the Company. Nothing contained in this letter, the Employment, Confidential Information,
Invention Assignment, and Arbitration Agreement, or the Stock Purchase Agreement will be construed as conferring upon you any right to remain employed by the Company or affect the right of the Company to terminate your employment at any time. Upon
your termination of employment, the Company will pay to you your salary through your date of termination and such other benefits in which you are vested or are otherwise entitled through the date of your termination. Except as expressly provided
above, the Stock Purchase Agreement or by law, the Company will have no further obligations to you following your termination of employment. 
  

			
	 Phone: 608-218-7600
 FAX: 608-218-7601
	  	info@nimblegen.com
www.nimblegen.com

 7. Miscellaneous. 
 (a) This agreement will be binding on the Company and its successors and will insure to the benefit of and be enforceable by your personal or legal representatives, heirs and successors. 
 (b) This agreement and all questions of its interpretation, performance and enforcement and the rights and remedies of parties will be determined in
accordance with the laws of the State of Wisconsin without application of conflict of law principles. 
 (c) This agreement supersedes any
and all prior agreements, whether written or oral, between the Company or any representative thereof and you relating to the services performed by you for the Company or your compensation for such services, and all such prior agreements are null and
void. 
 (d) Any notice required or permitted to be given under this agreement will be in writing and will be deemed given by: (a) upon
personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered
or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt at the following addresses or
to such other addresses either party shall specify by like notice: 
 if to the Company: 
 President and Chief Executive Officer 
 NimbleGen Systems Inc. 
 1 Science Court 
 Madison, WI 53711 
 with a
copy to: 
 Kenneth C. Hunt Esq. 
 Godfrey & Kahn, S.C. 
 780 North Water Street 
 Milwaukee, Wisconsin 53202 
 and if to you: 
 Mr. Steven W. Smith 
 2854 Richardson Street 
 Fitchburg, WI 53711 
 (e) The Agreement may be amended or modified only upon the written consent of the
Company and you. 
  

			
	 Phone: 608-218-7600
 FAX: 608-218-7601
	  	info@nimblegen.com
www.nimblegen.com

 (f) You hereby represent and warrant to the Company that (a) neither the execution of this Agreement
by you nor the performance of any of your obligations or duties hereunder will conflict with or violate or constitute a breach of the terms of any employment or other agreement to which you are a party or by which you are bound, and (b) you are
not required to obtain the consent of any person, firm, corporation or other entity in order to enter into this Agreement or to perform any of your obligations or duties hereunder. 
 If this letter correctly sets forth your understanding of our agreement, please sign a copy in the space provided below and return it to the Company.

  

	
	Very truly yours,
	
	NIMBLEGEN SYSTEMS INC.
	
	/s/ David C. Sneider
	David C. Sneider
	Vice-President and CFO

  

	
	 I confirm my agreement with
 the terms and conditions of
letter.

	
	/s/ Steven W. Smith
	
	Date: September 26, 2001

  

			
	 Phone: 608-218-7600
 FAX: 608-218-7601
	  	info@nimblegen.com
www.nimblegen.com

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