In two regions of Chile approximately one third of the population is indigenous. In the schools of these regions, students of indigenous backgrounds experience learning difficulties because their language, worldview and episteme are not held in consideration. This article aims to empirically demonstrate whether there is a relationship between the percentage of indigenous students enrolled in an educational institution and the average performance of schools on national standardized tests. To this end, a quantitative ex post facto method with a non-experimental cross-sectional and correlational design was used. The results show that there is a negative correlation between the results in standardized mathematics and language tests and the percentage of indigenous students in educational institutions; the ethnic factor is a predictor that explains a small part of the results in standardized tests; and educational institutions with a low percentage of indigenous students have significantly higher results in standardized tests than those with a high percentage of indigenous students. In conclusion, schools with a high concentration of indigenous students achieve poorer academic results than those with fewer indigenous students in the two macro areas of Chile that have a large indigenous population.