In a context of high rates of intimate partner violence (IPV), trials of female-controlled technologies for HIV prevention such as microbicides may increase the possibility of social harms. Seeking to explore the relationship between IPV and microbicide use further, this paper documents women's narratives of participating in the Microbicide Development Program (MDP) trial in Johannesburg, South Africa, and experiences of partner violence and conflict. A social science sub-study, nested within the trial, was conducted between September 2005 and August 2009, and 401 serial in-depth-interviews were undertaken with 150 women. Using coded interview transcripts, we describe the distribution of IPV and the possible association thereof with microbicide gel use and trial participation. More than a third of these 150 women reported IPV, of which half the cases were related to involvement in the trial. In their narratives, those women reporting IPV cast their partners as authoritarian, controlling and suspicious and reported verbal abuse, abandonment, and in some cases, beatings. Shared experiences of everyday violence shaped women's feelings of unease about revealing their participation in the trial to intimate partners and attempted concealment further contributed to strains and conflict within relationships. Our findings point to the role of social scientific enquiry in identifying the less obvious, hidden negative impacts of participation in a clinical trial therefore exposing limitations in the biomedical construction of 'social harms', as well as the implications thereof for potential future use outside the clinical trial setting.