Situations of chronic conflict across the globe make it imperative to draw attention to its gendered health consequences, particularly the violation of women's reproductive and sexual rights. Since early 2002 in Gujarat, western India, the worst kind of state-sponsored violence against Muslims has been perpetrated, which continues to this day. This paper describes the history of that violence and highlights the mental and physical consequences of sexual and gender-based violence and the issues that need to be addressed by the police, the health care system and civil society. It draws upon several reports, including from the International Initiative for Justice and the Medico Friend Circle, which documented the reproductive, sexual and mental health consequences of the violence in Gujarat, and the lacunae in the responses of the health system. The paper calls for non-discrimination to be demonstrated by health personnel in the context of conflict and social unrest. Their training should include conflict as a public health problem, their roles and responsibilities in prevention, treatment and documentation of this "disease", and focus on relevant medico-legal methodology and principles, the psychological impact of sexual assault on victims, and the legal significance of medical evidence in these cases.