AMENDMENT TO NONCOMPETITION AGREEMENT

THIS AMENDMENT TO NONCOMPETITION AGREEMENT (this “Amendment”) is executed and
made effective as of the 16th day of December, 2008, by and between TomoTherapy
Incorporated, a Wisconsin corporation (the “Company”), and the undersigned
employee (“Employee”), and amends the Noncompetition Agreement (the “Agreement”)
between the Company and Employee dated April 1, 2007.

RECITALS

The Employee tendered to the Company his resignation as the President of the
Company on December 10, 2008, effective December 31, 2008. The Employee is
willing to extend his term of noncompetition to thirty-two months
post-termination in consideration for the Company to accelerate all of his
unvested stock options and to allow the restrictions to lapse on all of his
restricted stock effective December 31, 2008. Thirty-two months from the
termination date runs through August 31, 2011, coinciding with the month in
which the last of Employee’s equity grants would have otherwise vested.

AGREEMENT

In consideration of the recitals and agreements set forth herein, Employee and
the Company agree that:

1. The first paragraph of Section 2 of the Agreement is hereby deleted and
replaced with the following:

“Non-competition. For a period of thirty-two (32) months commencing on the
termination of Employee’s employment with the Company, regardless of the reason
for such termination, the Employee shall not, either on Employee’s own behalf or
on behalf of any other person, association or entity, do any of the following:
develop, design, produce, plan, test, perform, evaluate, or sell, or supervise,
advise, manage or direct a person or entity in developing, producing, designing,
planning, testing, performing, evaluating, or selling a Competing Product.”

2. The Board of Directors shall cause Company management to take all such
actions necessary and proper to: 1) cause the restrictions to lapse on all of
the shares granted under the Restricted Stock Award Grant Notice and Restricted
Stock Agreement dated August 28, 2008, and 2) accelerate the vesting of all of
the shares granted under the Stock Option Agreement dated November 17, 2005
between Employee and the Company, effective upon the close of the NASDAQ market
on December 31, 2008.

3. Except as otherwise provided in this Amendment, all terms and conditions
previously set forth in the Agreement shall remain in effect as set forth
therein and all defined terms used in this Amendment shall have the same meaning
as indicated in the Agreement. In the event that this Amendment and the
Agreement are inconsistent, the terms and provisions of this Amendment shall
supercede the terms and provisions of the Agreement, but only to the extent
necessary to satisfy the purpose of this Amendment. Each party hereto represents
to the other that it has the full authority to execute, deliver and perform this
Amendment in accordance with its terms.

IN WITNESS WHEREOF, the parties have executed this Amendment on the date first
written above.

THE COMPANY:

TOMOTHERAPY INCORPORATED

By: /s/ Frederick A. Robertson
Frederick A. Robertson, M.D.
Chief Executive Officer

EMPLOYEE:

/s/ Paul J. Reckwerdt
Paul J. Reckwerdt