BACKGROUND:: This study provides population-based estimates of HIV prevalence and factors associated with HIV infection among MSM in three large cities in Nigeria. We aimed to increase the knowledge base of the evolving HIV epidemic among MSM, highlight risk factors that may fuel the epidemic, and inform future HIV prevention packages. METHODS:: A total of 712 MSM, aged 18 and older, living in Abuja, Ibadan and Lagos were recruited using respondent-driven sampling. Participants completed a behavioral questionnaire and tested for HIV. Population-based estimates were obtained using RDSAT software. Factors associated with HIV infection were ascertained using multiple logistic regression, adjusting for RDSAT individualized weights. RESULTS:: A high proportion of MSM reported high-risk behaviors, including unprotected anal sex with men (30-50%), unprotected vaginal sex with women (40%), bisexual behavior (30-45%) and never been tested for HIV (40-55%). The population-based estimates of HIV among MSM in the 3 cities were 34.9%, 11.3% and 15.2%, respectively. In Abuja, HIV was significantly associated with unprotected sex and transactional sex. In Ibadan, HIV was significantly associated with unprotected sex and self-identified bisexual. In Lagos, HIV was significantly associated with older age. CONCLUSION:: HIV prevalence among MSM in the three cities was 4 to 10 times higher than the general population prevalence and was behaviorally linked. In response to a complex set of risks and disadvantages that put African MSM at a greater risk of HIV infection, future interventions targeting MSM should focus on a comprehensive approach that combines behavioral, biomedical and structural interventions.