Recent efforts to develop and implement progressive models of transitional justice have been significantly influenced by major developments in the law concerning sexual violence in armed conflict. In particular, the International Criminal Tribunal for the former Yugoslavia has pioneered accountability for sexual violence against women in armed conflict. This article takes the ICTY as a case study of how gender can structure the accountability mechanisms of transitional justice. The article analyses how legal norms and practices instantiate and reiterate, rather than transform, existing hierarchical gender relations. It considers the existing models of sexual violence as a criminal harm under international law, and then examines gendered patterns of legal practice in ICTY prosecutions. To address this engendering of transitional justice, the article produces a new model of the harm of sexual violence in conflict, suggests the development of a new international offence of sexual violence and generates different strategies for international prosecutions of sexual violence.