A number of Latin-American indigenous organizations are striving to build autonomous indigenous and communitarian universities. According to indigenous leaders from all over the continent, 'Occidental' or 'Northern' ways of producing knowledge exclude by default many forms of indigenous knowledges. From an indigenous perspective, scientists need to think seriously about developing research methodologies that do not automatically discard indigenous knowledges. In this article I look at the emerging network of indigenous and communitarian universities in Latin America and ask how the universities seek to produce indigenous and communitarian research processes and methodologies. How do these methodologies differ from methodologies taught at 'Occidental' universities? As the global indigenous movement grows in confidence and strength, researchers trained and formed in traditional methodologies wanting to work with indigenous peoples, movements, organizations and communities, will increasingly be confronted with research methodologies that are profoundly different from what they are accustomed to.