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This study describes characteristics of academic inbreeding in the Brazilian higher education system. Results show the rate of inbreeding significantly differs among distinct types of institutions, fields of knowledge, states and university ranking tiers. According to this study, inbreeding is most likely to be found in established elite research institutions, concentrated in the Southeast of Brazil, in the STEM fields. These also happen to be the main providers and most prestigious consumers of the well‐trained local academic workforce, supporting the conclusion that both internal and external factors could be influencing the high concentration of inbred scholars at prominent alma maters. It contributes to international literature by evaluating the role of individual characteristics and by showing how the expansion of higher education to more geographically distant areas may establish different patterns of inbreeding.