This paper analyses the relationship between studies on the health of indigenous people in public health and public policies aimed at reducing ethnic-racial inequalities. This selection assumes that scientific production on the subject is part of the societal effort to confront health inequities and guarantee the rights and public policies of indigenous people. In total, 3,417 papers were found between 1956 and 2018, and 418 were selected for analysis from systematic literature mapping in the PubMed/Medline, Scopus, Lilacs, Sociological Abstract, and Web of Science databases. Initially, the literature is marked by the biomedical benchmark. After 1990, publications and dialogue with the human and social sciences are expanded, including the analysis of the implementation of indigenous health policy. We identified that the knowledge produced is associated with the political, social, and scientific transformations of the health reform and the indigenous agenda. Scientific production increased in 2010. We can conclude that the knowledge guiding the scientific production on indigenous health was established from a horizon politically implicated with the studied populations and improved Indigenous Health Subsystem.