In 1888, Altamirano was appointed as the first director of the National Medical Institute of Mexico. He held this position until his death. There, he installed the first laboratory of physiology in Mexico. During this period, he also made numerous trips of medical botany to different regions of the country, some in the company of internationally renowned botanists as Joseph Nelson Rose, Cyrus Pringle and George Russell Shaw. Additionally, Altamirano conducted numerous investigations, reported on the two journals of the institute: "El Estudio" and "Anales del Instituto Médico Nacional". On the other hand, he was responsible for the Institute's involvement in the Exposition Universelle (1889), held in Paris, and in the 1904 Louisiana Purchase Exposition, held in St. Louis, Missouri, and participated in several international conferences, such as the Ninth International Congress of Hygiene and Demography, held in Madrid from 10 to 17 April 1898. He established links with leading scientific institutions in Europe, U.S. and Latin America.