MADISON, Wis., March 16, 2007 — NimbleGen Systems today announced that it has filed a registration statement with the Securities and Exchange Commission relating to the proposed initial public offering of its common stock. The number of shares to be offered and the price range for the offering have not yet been determined.

J.P. Morgan Securities Inc. will serve as the sole book-running manager for the offering. Thomas Weisel Partners LLC is acting as co-lead manager, and Leerink-Swann & Company and Robert W. Baird & Co. are acting as co-managers for the offering.

A registration statement relating to these securities has been filed with the Securities and Exchange Commission, but has not yet become effective. These securities may not be sold nor may offers to buy be accepted prior to the time the registration statement becomes effective. This press release shall not constitute an offer to sell or the solicitation of an offer to buy nor shall there be any sale of these securities in any state in which such offer, solicitation or sale would be unlawful prior to their registration or qualification under the securities laws of any such state.

When available, copies of the preliminary prospectus relating to this offering may be obtained by contacting J.P. Morgan Securities Inc., 4 Chase Metrotech Center, CS Level, Brooklyn, NY 11245.

About NimbleGen Systems, Inc.
For more information about NimbleGen, please visit the company’s website at www.nimblegen.com.

NimbleGen Systems Inc. Media Contact:
Joleen Rau
Senior Director, Marketing Communications
608-218-7623