Background: Gender based violence, including violence by an intimate partner, is a major global human rights and public health problem, with important connections with HIV risk. Indeed, the elimination of sexual and gender based violence is a core pillar of HIV prevention for UNAIDS. Integrated strategies to address the gender norms, relations and inequities that underlie both violence against women and HIV/AIDS are needed. However there is limited evidence about the potential impact of different intervention models. This protocol describes the SASA! Study: an evaluation of a community mobilisation intervention to prevent violence against women and reduce HIV/AIDS risk in Kampala, Uganda. Methods/Design: The SASA! Study is a pair-matched cluster randomised controlled trial being conducted in eight communities in Kampala. It is designed to assess the community-level impact of the SASA! intervention on the following six primary outcomes: attitudes towards the acceptability of violence against women and the acceptability of a woman refusing sex (among male and female community members); past year experience of physical intimate partner violence and sexual intimate partner violence (among females); community responses to women experiencing violence (among women reporting past year physical/sexual partner violence); and past year concurrency of sexual partners (among males). 1583 women and men (aged 18–49 years) were surveyed in intervention and control communities prior to intervention implementation in 2007/8. A follow-up cross-sectional survey of community members will take place in 2012. The primary analysis will be an adjusted cluster-level intention to treat analysis, comparing outcomes in intervention and control communities at follow-up. Complementary monitoring and evaluation and qualitative research will be used to explore and describe the process of intervention implementation and the pathways through which change is achieved. Discussion: This is one of few cluster randomised trials globally to assess the impact of a gender-focused community mobilisation intervention. The multi-disciplinary research approach will enable us to address questions of intervention impact and mechanisms of action, as well as its feasibility, acceptability and transferability to other contexts. The results will be of importance to researchers, policy makers and those working on the front line to prevent violence against women and HIV.