Studies of indigenous peoples are a crucial part of genomic research, not only to define the extent of human diversity but to provide medical benefit to all people. There are more than 370 million indigenous people living in almost half the countries of the world. Exploding interest in indigenous genomics and global population structure has raised debate about issues of informed consent and community benefit. As was evident in March 2011 during the African and Southern African Society of Human Genetics Meeting in Cape Town, South Africa, the inclusion of indigenous people in future genomic research is paramount, but ethical guidelines must address local concerns. Scientific practices and values must be integrated with indigenous governance so that such genomic research can continue, with the benefits fully realized by all.