South Africa has some of the highest levels of both HIV and gender-based violence (GBV) worldwide. The international literature has highlighted the importance of tackling GBV in the fight against AIDS. Although the link between these epidemics is acknowledged by South Africa's medical and NGO communities, government response has largely dealt with them separately. PEPFAR is South Africa's largest HIV/AIDS donor, representing significant funding potential for programmes seeking to tackle these twin epidemics. Using a combination of policy document analysis and key informant interviews at national and provincial level (Western Cape), we examined PEPFAR's response to the GBV-HIV link, the extent to which PEPFAR is aligned to national policies and the extent to which implementing agencies have felt able to work with PEPFAR funding. A number of PEPFAR-South Africa's positions (e.g. on condoms and abortion) stand in contradiction to South Africa's own laws. While PEPFAR-South Africa officials are adamant that PEPFAR addresses the GBV-HIV link, it does not form an explicit strategic goal and there are no indicators for this work. Although some agencies receiving PEPFAR funding do address the links between GBV and HIV, this appeared incidental rather than the reason for their receipt of PEPFAR funding. Not one implementing agency interviewed agreed with PEPFAR's ideological stance, perceiving it unhelpful and inappropriate in a social context defined by violence and HIV. Nevertheless, many organizations were prepared to apply for funding. Those awarded it found creative ways to work with-or around-PEPFAR's restrictions to ensure delivery of an appropriate range of much needed services to those facing the twin epidemics of HIV and GBV. The recent change in the US administration offers an important opportunity for broader links between HIV and GBV to be supported through PEPFAR. This paper makes recommendations for building a more systematic approach on the current ad hoc experience of PEPFAR in South Africa.