A common criticisms of school choice programs is that, instead of improving student achievement, they would increase school segregation. Parents may use different criteria to choose a school, such as proximity, school quality, or the school's ethnic/racial composition. As a result, the system would be segregated based on the parent's preferences. This research examines the school preferences of indigenous parents and whether ethnic discrimination influences their decision-making process. Longitudinal national-level data from Chile were analyzed using OLS with fixed effects. The results show that indigenous students, particularly those who have suffered ethnic discrimination in middle school, prefer high schools with a higher percentage of indigenous students. Furthermore, it was found that the level of acts of discrimination occurring in middle schools increases as the percentage of indigenous students rises. However, when the proportion of indigenous and non-indigenous students is similar, indigenous students are less likely to face discrimination.