Research on interventions to prevent HIV and other sexually transmitted infections (STIs) is heavily influenced by participant reporting of sexual behavior, despite uncertainty about its validity. Exclusive reliance on participant self-report often is based, overtly or by implication, on 4 assumptions: (1) no feasible alternatives exist; (2) misreporting can be minimized to levels that can be disregarded; (3) misreporting tends to underreport sensitive behaviors; and (4) misreporting tends to be nondifferential with respect to the groups being compared. The objective of this review are to evaluate these assumptions, including a review of studies using semen biomarkers to evaluate the validity of self-reported data, and to make recommendations for applying biological markers of semen exposure detectable in women to further strengthen research on HIV/STI prevention. Increasing evidence shows that semen biomarkers provide an important means of assessing and augmenting the validity of studies on HIV/STI prevention. Additional biomarkers are needed to assess male exposure to vaginal sex and both male and female exposure to anal sex. Methods and study designs that incorporate biomarkers into studies collecting self-reported behavioral data should be considered where possible.