This study examines levels and correlates of internalized homophobia among men who have sex with men (MSM) in Pretoria, South Africa. Using respondent-driven sampling, we recruited 324 MSM from February to August 2009. Results were adjusted using RDSAT analysis to yield population-based estimates. High levels of internalized homophobia exist among South African MSM: 10–15% reported “often/very often” and over 20% reported “sometimes” having feelings of internalized homophobia. A greater level of internalized homophobia was significantly associated with a lower level of education [Adjusted Odds Ratio = 2.2; 95% CI = 1.1–4.9], a higher level of HIV misinformation [AOR = 2.7; 95% CI: 1.3–5.3], bisexual identity (vs. homosexual) [AOR = 5.5; 95% CI: 2.5–12.0], and HIV-related conspiracy beliefs [AOR = 2.4; 95% CI: 1.02–5.8]. These findings contribute valuable information to our understanding of internalized homophobia in South Africa, highlighting the need to empower the gay community, promote self-acceptance of homosexual identity, and address conspiracy beliefs among MSM to reduce internalized homophobia and increase access to HIV prevention interventions.