**Exhibit 31.2****Certifications**I, Stephen C. Hathaway, certify that:1. I have reviewed this report on Form 10-Q of TomoTherapy Incorporated:2. Based on my knowledge, this report does not contain any untrue statement of a material fact oromit to state a material fact necessary to make the statements made, in light of the circumstancesunder which such statements were made, not misleading with respect to the period covered by thisreport;3. Based on my knowledge, the financial statements, and other financial information included inthis report, fairly present in all material respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in this report;4. The registrant’s other certifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a—15(e) and 15d—15(e)) andinternal control over financial reporting (as defined in Exchange Act Rules 13a—15(f) and15d—15(f)) for the registrant and have:(a) Designed such disclosure controls and procedures, or caused such disclosure controlsand procedures to be designed under our supervision, to ensure that material informationrelating to the registrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which this report is beingprepared;(b) Designed such internal control over financial reporting, or caused such internalcontrol over financial reporting to be designed under our supervision, to providereasonable assurance regarding the reliability of financial reporting and the preparationof financial statements for external purposes in accordance with generally acceptedaccounting principles;(c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of the disclosure controlsand procedures, as of the end of the period covered by this report based on suchevaluation; and(d) Disclosed in this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter (theregistrant’s fourth fiscal quarter in the case of an annual report) that has materiallyaffected, or is reasonably likely to materially affect, the registrant’s internal controlover financial reporting; and5. The registrant’s other certifying officer and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’s auditors and the auditcommittee of the registrant’s board of directors (or persons performing the equivalent functions):(a) All significant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely to adversely affectthe registrant’s ability to record, process, summarize and report financial information;and(b) Any fraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financial reporting.Date:June 15, 2007                                                           /s/ Stephen C. Hathaway   Chief Financial Officer and Treasurer   TomoTherapy Incorporated