Increased use of intensity modulated radiation therapy (IMRT) has resulted in increased efforts in patient quality assurance (QA). Software and detector systems intended to streamline the IMRT quality assurance process often report metrics, such as percent discrepancies between measured and computed doses, which can be compared to benchmark or threshold values. The purpose of this work is to examine the relationships between two different types of IMRT QA processes in order to define, or refine, appropriate tolerances values. For 115 IMRT plans delivered in a 3 month period, we examine the discrepancies between (a) the treatment planning system (TPS) and results from a commercial independent monitor unit (MU) calculation program; (b) TPS and results from a commercial diode-array measurement system; and (c) the independent MU calculation and the diode-array measurements. Statistical tests were performed to assess significance in the IMRT QA results for different disease site and machine models. There is no evidence that the average total dose discrepancy in the monitor unit calculation depends on the disease site. Second, the discrepancies in the two IMRT QA methods are independent: there is no evidence that a better —or worse—monitor unit validation result is related to a better—or worse—diode-array measurement result. Third, there is marginal benefit in repeating the independent MU calculation with a more suitable dose point, if the initial IMRT QA failed a certain tolerance. Based on these findings, the authors conclude at some acceptable tolerances based on disease site and IMRT QA method. Specifically, monitor unit validations are expected to have a total dose discrepancy of overall, and per beam, independent of disease site. Diode array measurements are expected to have a total absolute dose discrepancy of overall, and per beam, independent of disease site. The percent of pixels exceeding a and 3 mm threshold in a gamma analysis should be greater than or equal to for non-head and neck IMRT cases, and for head and neck IMRT cases. The IMRT QA methodology described here is neither unique nor ubiquitous, and the ability to deliver a safe IMRT does not simply require IMRT QA tests to pass a given tolerance; however, the selection of a tolerance should be meaningful when assessing a complex plan. The methodology in defining appropriate tolerances, described in this article, is based on an interpretation of IMRT QA results from IMRT plans deemed safe to deliver.