We conducted a respondent driven sampling survey to estimate HIV prevalence and risk behavior among men who have sex with men (MSM) in Unguja, Zanzibar. Men aged ≥ 15 years living in Unguja and reporting anal sex with another man in the past 3 months were asked to complete a questionnaire and provide specimens for biologic testing. HIV prevalence was 12.3% (95% confidence interval 8.7, 16.3). HIV infection was associated with injecting drugs in the past 3 months, Hepatitis C virus infection and being paid for sex in the past year. Interventions for MSM in Zanzibar are needed and should include linkages to prevention, care and treatment services.