Young men who have sex with men (YMSM) face a disproportionately high burden of HIV. Oral pre-exposure prophylaxis (PrEP) is effective in preventing HIV acquisition, but adherence to PrEP among YMSM may be inadequate. Medication adherence may be assessed via biomarkers, which are expensive and invasive, or via self-report through Audio Computer Assisted Self-Interview (ACASI), which may result in over-reporting of adherence. In this paper we assess the potential of a new method of self-report, the Interactive Questionnaire System (iQS), in validly estimating true adherence rates. PrEP adherence among 167 YMSM aged 15-23 was measured via dried blood spot (DBS), ACASI, and iQS twice over a 24-week study period. Both ACASI- and iQS-reported data revealed that over 40% of individuals self-reporting adequate PrEP adherence had DBS-estimated drug levels indicating inadequate adherence. Adjusted logistic repeated measures random intercept regression analyses indicated that younger YMSM had higher odds of over-reporting adherence than older YMSM-each 1 year increase in age was associated with 0.79 times the odds of over-reporting adherence (95% CI 0.63, 0.98; p value = 0.031), and being African American was associated with 3.22 times greater odds of over-reporting than non-African Americans (95% CI 1.51, 6.90; p-value = 0.0003). These results suggest that ACASI and iQS methods of self-report significantly overestimate true PrEP adherence rates among YMSM, and that the odds of over-reporting adherence may be affected by both age and race.