In 1990, the Brazilian Unified Health System institutionalized new relationships between the government and society. In recognition of the inequalities and inequities inflicted upon Indigenous Peoples, the Indigenous Health Subsystem was established in 1999. Roles were created for the democratic exercise of Indigenous participation and prominence in three border spaces: Indigenous health agents as members of health teams; Indigenous representatives on health councils; and Indigenous organizations as primary care providers. This article explores these spaces based on ethnographic research from southern Brazil. It concludes that the roles created for Indigenous participation and governance are ambiguous and contradictory. When participating in new opportunities created by the government, Indigenous actors are subjected to a centralized and bureaucratized system that offers little possibility of autonomous decision-making or action.