School segregation, understood as the unequal distribution of students in schools based on their personal or social characteristics, is an element of educational equity with a clear impact on social injustice that has not been deeply studied in Latin America. This article presents a methodological guide on the use of different schooling segregation index available to estimate its magnitude. There is debate about the advantages and limitations of each index. Similarly, the magnitude of school segregation by socioeconomic status in Primary Education in Latin America is determined. Index of Dissimilarity, Gorard, Isolation, Square Root and Socio-Economic Inclusion analysed with different criteria forming the minority group: P10, Q1 and Q4. The results provide a broad discussion on the potential of each index. The use of the index of socioeconomic inclusion defends as well as the use of average between Q1 and Q4 to get an overall picture of the phenomenon. For this, the TERCE database is used, and high magnitude of school segregation in Latin America are offered.