This article provides a historical and comparative study of the role that management of inequalities has played in the formation and evolution of educational institutions in three countries: Costa Rica, Cuba and Guatemala. This particular focus shows that this function has played a determining role, even if its organization has varied deeply in time and space. Thus, three important phases are identified, depicted by different educational modalities of management of inequalities: the liberal period, the period of extended management of inequalities, and the neo-liberal period. Yet, compared with the relative synchrony of these changes, evolutions of the relation between education and inequalities show sharp contrasts. This divergence can be explained by taking into account the interrelations between educational institutions, economic structures and behaviours of the actors.