Multiple studies connect ethnic background with uneven educational outcomes; this study contributes a novel perspective to the literature by attending to indigenous peoples’ experiences with vertical and horizontal dimensions of stratification in the Chilean school system. In particular, I investigate the transition from primary to secondary school and to higher education, comparing enrollment in academic and vocational tracks at the secondary and tertiary levels. With a series of logistic regressions, I study differences in these critical educational transitions associated with indigenous status, together with gender and location. Analyses of the 2012 seventh-grade cohort show that indigenous status increases the likelihood of enrolling in vocational high schools, but regarding the transition to higher education, indigenous status is only relevant when school SES is not included. Nevertheless, vocational high school graduates (where indigenous students concentrate) are less likely to enroll in higher education, and more likely to enroll in vocational instead of academic higher education programs. Overall, indigenous status has a clear impact on students' transition from middle school to high school, which has relevant consequences for the transition to higher education.