Same-sex practices are stigmatized in much of sub-Saharan Africa. Cross-sectional relationships between discrimination, access to and use of health care services, and HIV knowledge among men who have sex with men (MSM) were assessed in Malawi, Namibia, and Botswana. A survey and HIV screening were used to explore these variables and the prevalence of HIV. Overall, 19% of men screened positive for HIV infection. Ninety-three percent knew HIV is transmitted through anal sex with men, however, only 67% had ever received information of how to prevent this transmission. Few (17%) reported ever disclosing same sex practices to a health professional and 19% reported ever being afraid to seek health care. Men reported ever been denied health care services (5%) and 21% had ever been blackmailed because of their sexuality. Strong associations were observed between experiences of discrimination and fear of seeking health care services. Characterizing the relationship between stigma and health care seeking practices and attitudes can inform the development and implementation of HIV interventions for African MSM.