They are one of the most vulnerable, stigmatised and neglected groups and in some parts of the continent, carry the highest rate of HIV infection.
The most recent Human Sciences Research Council (HSRC) study of three cities found that HIV prevalence was significantly higher among MSM than in the general population. In Durban it was as high as 48.2 percent.
Policy developers, programme implementers, donor representative, researchers and ambassadors gathered for an MSM technical forum to discuss new evidence on HIV prevention services and access (to services) for MSM.
The forum will review recent data on trends in HIV transmission among African MSM, with representatives from Africa and other Eastern and Southern African countries sharing expertise and experiences.
"Many countries in Eastern and Southern Africa have included MSM as key populations but few have actual programmes in place that are implemented. South Africa and Kenya are the two exceptions to the rule. Kenya, despite it being illegal - programmes are provided under the human rights umbrella", said Professor Larry Gelman (crt), from the University of Maritoba, Canada.
Further, Gelman said, in most countries in sub-Saharan Africa, the population of MSM was unknown with many MSM reluctant to be studies in the countries where same-sex behaviour is criminalised.
Professor James McIntyre (crt) Ceo of the Anova Health Institute, said, "In South Africa, we do not have the legal barriers many other African countries do but we do have a very vulnerable population of MSM."
The institute established Health4Men - a project to facilitate services for MSM - in 2008.
It provides direct clinical services in partnership with the National Department of Health, having established Africa's first Centre of Excellence: Ivan Toms Centre for Men's Sexual Health in Cape Town.
Today, in Johannesburg and Cape Town, over 20 000 patients are registered at the two sites.
Dr Kevin Rebe, an HIV clinician and researcher at Anova, said SA was fortunate in that the government did view MSM as a key population and also sponsored PrEP through the department of health.
Currently a two year demonstration project is underway (which started in July 2015) to assess the feasibility of delivering nurse-driven PrEP for MSM at a primary healthcare level as part of the combination HIV prevention strategy.
The aim of the demonstration study isn't to show PrEP works, but to use the current guidelines in 'real-world' settings - being public clinics.
Rebe said they hoped to recruit 400 MSM at two sites - one in Joburg the other in Cape Town.
One of their secondary aims was to assess the knowledge, acceptability, and uptake of PrEP and other HIV prevention interventions among HIV-negative MSM.