0001193125-07-124282 Sample Contracts

NIMBLEGEN SYSTEMS INC. AWARD AGREEMENT
Award Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses • Wisconsin

This Award Agreement, entered into as of October 7, 2005 (the date of grant), is between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Daniel Clutter (the “Participant”). All terms used herein and not otherwise defined shall have the same meaning as set forth in the Company’s 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended (the “Plan”).

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NIMBLEGEN SYSTEMS INC. AWARD AGREEMENT
Award Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses • Wisconsin

This Award Agreement, entered into as of October 7, 2005 (the date of grant), is between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Stanley D. Rose (the “Participant”). All terms used herein and not otherwise defined shall have the same meaning as set forth in the Company’s 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended (the “Plan”).

STOCKHOLDER AGREEMENT WITH NIMBLEGEN SYSTEMS INC. (Applicable to Shares Purchased By Exercise of Stock Options)
Stockholder Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses

This Stockholder Agreement (the “Agreement”) dated as of October 19, 2005, is by and between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and the person whose name appears on the signature page hereof (“Participant”).

NIMBLEGEN SYSTEMS, INC. SEVENTH AMENDED AND RESTATED STOCKHOLDERS AGREEMENT January 25, 2007
Stockholders Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses • Delaware

This SEVENTH AMENDED AND RESTATED STOCKHOLDERS AGREEMENT (this “Agreement”) is entered into as of January 25, 2007, by and among NIMBLEGEN SYSTEMS, INC., a Delaware corporation (the “Company”), the individuals and entities listed on Exhibit A (each individually a “Common Stockholder” and collectively the “Common Stockholders”), the individuals and entities listed on Exhibit B (each individually a “Series E Stockholder” and collectively the “Series E Stockholders”), and the individuals and entities listed on Exhibit C (each individually a “Series F Stockholder” and collectively the “Series F Stockholders”).

FIRST AMENDMENT TO SEVENTH AMENDED AND RESTATED STOCKHOLDERS AGREEMENT
Stockholders Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses

This First Amendment (this “Amendment”) amends that certain Seventh Amended and Restated Stockholders Agreement, dated as of January 25, 2007 (the “Agreement”), and is entered into as of April 6, 2007, by and among NimbleGen Systems, Inc., a Delaware corporation, the individuals and entities listed on Exhibit A who have executed a counterpart signature page hereto (each individually a “Common Stockholder” and collectively the “Common Stockholders”), the individuals and entities listed on Exhibit B who have executed a counterpart signature page hereto (each individually a “Series E Stockholder” and collectively the “Series E Stockholders”), and the individuals and entities listed on Exhibit C who have executed a counterpart signature page hereto (each individually a “Series F Stockholder” and collectively the “Series F Stockholders”).

Contract
Nimblegen Systems Inc • May 29th, 2007 • Optical instruments & lenses

NOTE: The information designated by a bracketed asterisk [*] has been omitted pursuant to a request for confidential treatment and has been filed separately with the Securities and Exchange Commission.

INDEMNIFICATION AGREEMENT
Indemnification Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses • Delaware

THIS INDEMNIFICATION AGREEMENT (“Agreement”) is made and entered into as of the day of , 20 , by and between NIMBLEGEN SYSTEMS, INC., a Delaware corporation (the “Company”), and (“Indemnitee”), to become effective in such manner and at such time as provided herein.

FORM OF STOCKHOLDER AGREEMENT WITH NIMBLEGEN SYSTEMS INC. (Applicable to Shares Purchased By Exercise of Stock Options)
Stockholder Agreement • May 29th, 2007 • Nimblegen Systems Inc • Optical instruments & lenses

This Stockholder Agreement (the “Agreement”) dated as of this day of , , is by and between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and the employee of the Company whose name appears on the signature page hereof (“Employee”).

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