The varied, abrupt and amazing geography of the land of Peru is home of one of the major concentrations of indigenous peoples in the world. The asymmetry of power, however, in their relationship with the rest of society and the State is still very evident in their social exclusion, their gap in social and economic development, barriers in their access to health services as well as their marginalization and exploitation as subjects of health research. In this paper, we analyse two cases of research on indigenous populations in Peru, discuss them from the point of view of bioethics and reflect on important issues for researchers, research participants and the society, such as the need to respect different cultures, the need that the research being done is relevant to the needs of the population in which it is conducted and the necessity to empower indigenous communities in participatory research, to strengthen the institutions and to protect human rights, namely through ethics committees for research and the free, informed and meaningful informed consent. This approach should foster quality research, while at the same time fully respecting human rights and bioethics. We cannot forget that advancements in genetics, throughout the world, are very much in debt to indigenous populations.