Despite the well established role of the health sector in responding to cases of sexual assault, this issue remains a blind spot in health care governance. With no standard protocols in place for managing such cases, women and children reporting sexual assault continue to receive substandard care, and malfunctions of the health system result in lack of justice. This paper draws on the experience of engaging with the health sector to develop a comprehensive response to survivors of sexual assault. In 2008, we implemented an action project to streamline procedures in responding to sexual assault, at two peripheral municipal hospitals in Mumbai. This included implementation of a kit for sexual assault examination and forensic evidence collection, capacity building of health care providers, and provision of psychosocial support for survivors. Several gaps were found, with regard to consent seeking, admission procedures, treatment, and coordination with police and forensic laboratories, that rendered services inadequate and often impinged on the autonomy of survivors. The lack of protocols for preserving evidence provided scope for tampering. Health professionals considered their role to be largely medico-legal, and their ethical responsibility towards caring for the patient was compromised Some problems we encountered were rectified through formulating standard operating protocols and guidelines, which both compelled doctors to adhere to them and empowered doctors to defend their good practices. We end by critiquing the recent moves made by the government to implement guidelines for such cases and suggest how this could be better accomplished if services are provided to survivors of sexual assault in an ethical and comprehensive manner.