People with innate variations of sex characteristics (also known as intersex traits or disorders or differences of sex development) have any of a wide range of innate physical traits that differ from medical and social norms for female and male bodies. Responses to these physical differences create experiences and risks of stigmatisation, discrimination, violence, and harmful medical practices intended to promote social and familial integration and conformity with gender stereotypes. As is evident globally, the Australian policy response to the existence and needs of people with innate variations of sex characteristics has been largely incoherent, variously framing the population as having disordered sex development in need of “fixing”, and a third sex/gender identity group in need of recognition, with only recent engagement by intersex community-controlled civil society organisations. This paper presents an overview of the context and goals of the intersex human rights movement in Australia. Australian intersex community organisations have sought to apply human rights norms and develop new infrastructure to address key health and human rights issues, and necessitating new ways of resolving policy incoherence. Together with human rights, mental health, and public health institutions, they have called for significant changes to medical models of care and reform to research and classification systems. Intersex community organising and resourcing have made a tangible difference. The Australian Capital Territory is the first jurisdiction in the country to move ahead with reforms to clinical practice, including a legislative prohibition of certain practices without personal informed consent, oversight of clinical decision-making, and investment in psychosocial support. A national community-controlled psychosocial support service has also commenced.