Health inequalities impact sex-variant people in highly differentiated ways. This is evidenced in much academic and activist intersex research documenting the highly specific forms of inequalities arising from misrecognition, discrimination and human rights abuses inherent to pathologised accounts of non-normative bodies. Important theoretical work further interrogates the implications of sex variant subjectivities, identities and bodies for static or binary notions of both sex and gender. In this paper, we aim to contribute further to this scholarship. We draw upon feminist materialist and Deleuzean-informed understandings of materials or matter to rethink debates over sex-variant subjectivities, identities and bodies in relation to inequalities in health. We argue ‘the turn to matter’ and associated new materialist theories draw attention to the complex, dynamic relational assemblages and entanglements mutually constituting the affective, embodied and socio-material worlds of intersex people. Informed by these theories, we propose that inequalities can be more fully addressed through a new health equity research agenda that is co-produced with sex-variant people. This agenda will enable a fuller exploration of the unsettling but transformative capacities of intersex matters and meanings with the contextually specific understandings of equity in relation to health and health care.