Little is known about how social factors influence vulnerability to, and consequences of, HIV infection among men who have sex with men (MSM) in South Africa. This study aimed to analyse social stratification and its links with HIV among MSM in Cape Town, South Africa. Six interviews and six focus group discussions (n = 25) were conducted. Tools were based on the World Health Organisation’s Commission on the Social Determinants of Health framework. Directed content analysis was used to analyse data. Race and education were directly linked to social position. MSM from lower social positions were more vulnerable to HIV, and had more negative consequences of HIV infection, compared to wealthier MSM. Engagement with community leaders, health workers and police to promote inclusion could reduce vulnerability of MSM to HIV. Increased access to free, non-discriminatory HIV-related services would reduce inequities in access to HIV services by MSM.