ABSTRACT To make a useful interpretation of the outputs from genome integrity assays, it is critical to know that they measure biological variability that is relevant to the disease endpoint of interest. Potential pitfalls for any assay include: i) the differences observed between people are transient (are not reproducible if repeated on a different occasion); ii) apparent differences in repair capacity are an artifact arising from the particular steps involved in an individual assay carried out on ex vivo samples; and iii) the differences between people are tissue-specific (genome integrity in blood cells might not predict genome integrity in other tissues). These pitfalls can be mitigated by cross-testing of assays, which have distinct strengths that make them less susceptible to one or more of these pitfalls. Each of our laboratories has developed and validated powerful cutting-edge genome integrity assays that rely on related yet independent biological principles. Mutation assays (Vijg) are more resistant to pitfall (i) because they measure the cumulative endpoint of a unidirectional process and therefore cannot vary from day to day. By contrast, functional assays may be subject to both experimental and biological variables that alter the apparent efficiency of DNA repair. Mutation assays are also resistant to pitfall (ii) because they report on processes that occur in vivo. However, it may not be possible to distinguish between mutations arising from increased environmental exposure versus inefficient DNA repair or endogenous lesions. Functional assays carried out ex vivo on tissue samples may be more susceptible to this pitfall. However, it is less likely that two different functional assays will be subject to the same artifact. The FM- HCR assay (Nagel) reports repair of transiently transfected episomal plasmid DNA with site-specific chemically defined DNA lesions, while the UDS assay (Niedernhofer) measures repair of genomic DNA with DNA damage induced by UV light. Thus, the assays operate under fundamentally different principles. All three of our assays may be subject to pitfall (iii), but this can be addressed by comparing assays in multiple tissues from the same individuals. Taken together, our proposed use of these three assays in this supplement provide a robust approach to test the pitfalls outlined above. We are well-positioned to delineate potential sources of error in our measurements and to establish a powerful platform for measuring genome integrity accurately.