[2][3] He returned to his home state, and practiced medicine in the town of Huatusco for ten years.
In his early years as a medical doctor, he became interested in local history and published a book on agrarian struggle during the colonial era.
[4] In 1942 he met Columbia University-trained anthropologist Manuel Gamio, who suggested that Aguirre Beltrán study blacks in Mexico, resulting in his landmark study, La población negra de México, 1519-1810: Estudio etnohistórico (1946).
He left the practice of medicine in favor of becoming an anthropologist, although he pursued topics on medical anthropology.
Under the administration of Luis Echeverría (1970–76) he was sub-secretary of the Department of Culture and Continuing Education, creating a publication series disseminating research on indigenous communities.