Identity is central for research on education since, under certain conditions, it may influence school choice, career preferences and classroom behaviour. Identity also determines disposition toward schooling because it may have the capacity to shape and modify the values, beliefs and characteristics that distinguish one person from another, by means of pedagogical practices and institutional arrangements. This article, therefore, examines the notion of identity that Amartya Sen proposed, and how it can be used to study the social and education disadvantages that indigenous people face in Mexico. This argument unfolds in four stages. The first part will discuss the notion of identity that Amartya Sen developed. The second will show some facts and figures about Mexico's indigenous population, while the third will stress some pervasive educational inequalities that ethnic groups face. The fourth, and final, part will present some results of an affirmative action program that a number of universities in Mexico have implemented. It concludes by showing that further analysis is required in order to obtain a broader understand of how identity is formed and transformed within education spaces and that this, ultimately, may advance the current notion of identity proposed by Sen.