Globally, men who have sex with men (MSM) continue to be disproportionately affected by the HIV pandemic. However, prior to this study, very little was known about the magnitude and factors that heighten MSM’s vulnerabilities to HIV and other STIs in Nigeria. A cross-sectional survey was administered to 1,125 consenting MSM in Lagos and Ibadan recruited through modified respondent driven strategy. Sero-prevalence of HIV, hepatitis B (HBV), hepatitis C (HCV) and syphilis and levels of unprotected anal intercourse (UAI) were determined using data adjusted for network size and unweighted data for the pooled sample. Correlates of HIV, HBV, HCV and UAI were examined using multiple logistic regression analyses. Results revealed relatively young sexually active men who engaged in multiple concurrent sexual relationships with both men and women. More than half of the men self-identified as bisexual, and 44.4% as homosexual. High levels of risky sexual behaviours were demonstrated with over two-thirds of MSM in Ibadan (65.5%) and Lagos (69.7%) reporting UAI with their male partners in the previous 6 months. Correlates of URAI included homosexual identity, older age, lack of social support, and douching. Prevalence of previously undiagnosed HIV infection were four times higher in Lagos 12.7% (95% CI 10.6-15.0), and Ibadan 11.2% (95% CI 5.7-16.2) than the national HIV prevalence among Nigerian men. Prevalence of HBV (10.1% and 18.0%); HCV (2.8% and 4.3%) and current active syphilis (0.03%) infections in Lagos and Ibadan respectively were also high. Correlates of HIV were URAI and UIAI with men and women, condom breakage, homosexual identity, increasing age, employment, sexual activities with non-African white men and internalized homophobia. Bisexual identity, UIAI with male sex partners, and low self-esteem were associated with HBV infection. Correlates of HCV were URAI and reported sex with men who had lower educational status. This study confirms the existence of MSM who engage in risky behaviours with very limited access to appropriate HIV and STI prevention services.