Item 1.01 Entry into a Material Definitive Agreement.

On April 10, 2009, TomoTherapy Incorporated (the "Company") entered into an Amendment One (the "Amendment") to the Manufacture and Supply Agreement (the "Supply Agreement") with an effective date of October 8, 2008, with Siemens AG Healthcare Sector, Components & Vacuum Technology, having a business address at Henkestrasse 127, 91052 Erlangen, Germany ("Siemens"), for the manufacture, purchase and sale of linear accelerators and related components. The Amendment is effective as of April 1, 2009.

The Amendment reduced the maximum price that Siemens could charge the Company to repair out-of warranty linear accelerator assemblies. The Amendment also provides that if a linear accelerator assembly cannot be repaired as determined by both Siemens and the Company, then Siemens will issue the Company a specified credit for the scrap value of the material. It also adds to the warranty provision that repaired out-of-warranty accelerator assemblies are warranted for twelve months from the date of delivery.

All other terms and conditions of the Supply Agreement remain in effect as set forth therein.

The foregoing discussion of the terms and conditions of the Amendment does not purport to be complete and is subject to and qualified in its entirety by, the full text of the Amendment, which is attached as Exhibit 10.1 hereto and incorporated herein by reference, as redacted in accordance with a request for confidential treatment.

Item 9.01. Financial Statements and Exhibits.

(d) Exhibits.

Number Description

10.1 * Amendment One to Supply Agreement with Siemens AG Healthcare Sector dated April 10, 2009, effective as of April 1, 2009

* Confidential treatment has been requested for portions of this exhibit. These portions have been omitted from the Form 8-K and submitted separately to the Securities and Exchange Commission.

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