This study assessed the level of internalized homophobia and associated factors among men who have sex with men (MSM) in Nigeria. Using respondent driven sampling, MSM were recruited in Lagos and Ibadan between July and September, 2006. Internalized homophobia was assessed as a negative composite score using an 11-item scale. A total of 1,125 MSM were interviewed. About 44.4% self-identified as homosexual or gay while 55% regarded themselves as bisexual. About a third of the respondents reported internalized homophobia. With homosexual/gay men as reference, respondents who self-identified as bisexual were two times more likely [AOR 2.1; 95 CI: 1.6 - 2.9, p < 0.001] to report internalized homophobia. Those who were HIV positive were also twice as likely to report internalized homophobia compared to those who were HIV negative [AOR 1.8; 95% CI: 1.2 - 2.7, p = 0.004]. As internalized homophobia impedes acceptance of HIV prevention programming, identifying MSM who experience internalized homophobia is integral to the success of HIV prevention programming in Nigeria.