Indigenous groups in Latin America face a double exclusion from higher education, with low levels of access to institutions and little acknowledgement of their distinctive cultural and epistemological traditions within the curriculum. This article assesses current policies in Mexico and Brazil towards indigenous populations in higher education, considering the various responses to the challenge, including affirmative action programmes in mainstream universities, intercultural courses and autonomous institutions. These policies and initiatives are analysed using the theoretical frames of redistribution and recognition, focusing on demands for formal equality and material wellbeing on the one hand, and a distinctive cultural and educational space on the other. While state-sponsored policies focus primarily on the redistributive element, initiatives based on recognition come largely from autonomous organisations, raising a series of dilemmas and tensions around educational justice for indigenous populations in the region.