To date, there is a dearth of surveillance data on the prevalence of HIV and associated risk behaviours among men who have sex with men (MSM) in South Africa. This is particularly true for data collected from several sites using the same sampling approach. This study called the Marang Men's Project was undertaken to fill this information gap. It was implemented among MSM in the three largest cities of South Africa, namely, Cape Town in the Western Cape, Durban in KwaZulu-Natal and Johannesburg in Gauteng. The high HIV prevalence estimates found in our study among MSM in each of the three study cities call for a need to implement a national HIV bio-behavioural surveillance programme for MSM. The Marang Men's Project has demonstrated that there is an urgent need for interventions, which respond not only to the heterosexual HIV epidemic but also to the HIV epidemic among MSM in South Africa. This survey therefore provides valuable information to SANAC, the national and provincial Departments of Health (DoHs), and lesbian, gay, bisexual, transgender and intersex (LGBTI) organisations to both implement and advocate for improved programmes for the health of MSM.