There are few studies of HIV risk behavior among men who have sex with men (MSM) in sub-Saharan Africa. We conducted a behavioral survey of MSM in peri-urban "township" communities in Gauteng province, South Africa. Between October 2004 and March 2005, 199 MSM completed an interviewer administered pen-and-paper standardized questionnaire. The sample was 94% black, 83% identified as gay, and 12% as bisexual. Among those reporting sex with other men in the prior six months (n = 147), 59% reported unprotected anal intercourse (UAI). Increased risk of UAI was associated with both regular drinking (adjusted odds ratio (OR) 4.1, 95% confidence interval (CI) 1.4, 12.6) regular drinking to intoxication (OR 2.6, 95% CI 1.0, 6.8), and reporting symptoms of rectal trauma resulting from anal intercourse (AI; OR 4.3, 95% CI 1.8, 10.4). Decreased risk of UAI was associated with the exclusive use of lubricants that are latex-compatible for AI (OR 0.3, 95% CI 0.1, 0.7). Township MSM in South Africa are at high risk of HIV infection. Targeted sexual health and risk reduction interventions that address the link between alcohol use and HIV risk are urgently needed.