We describe the utilization of health services by men who have sex with men (MSM) in South African cities, their perceptions of available health services, and their service preferences. We triangulated data from 32 key informant interviews (KIIs), 18 focus group discussions (FGDs) with MSM in four cities, and a survey of 285 MSM in two cities, recruited through respondent-driven sampling in 2008. FGDs and KIIs revealed that targeted public health sector programs for MSM were limited, and that MSM experienced stigma, discrimination, and negative health worker attitudes. Fifty-seven per cent of the survey participants had used public health services in the previous 12 months, and 69 per cent had no private health insurance, with no difference by HIV status. Despite these findings, South Africa is well placed to take the lead in sub-Saharan Africa in providing responsive and appropriate HIV services for MSM.