The AMM was established during the American Civil War as a center for the collection of specimens for research in military medicine and surgery. In 1862, Hammond directed medical officers in the field to collect "specimens of morbid anatomy ... together with projectiles and foreign bodies removed" and to forward them to the newly founded museum for study. The AMM's first curator, John Brinton, visited mid-Atlantic battlefields and solicited contributions from doctors throughout the Union Army. During and after the war, AMM staff took pictures of wounded soldiers showing effects of gunshot wounds as well as results of amputations and other surgical procedures. The information collected was compiled into six volumes of The Medical and Surgical History of the War of the Rebellion, published between 1870 and 1883.
During the late 19th and early 20th centuries, AMM staff engaged in various types of medical research. They pioneered in photomicrographic techniques, established a library and cataloging system which later formed the basis for the National Library of Medicine (NLM), and led the AMM into research on infectious diseases while discovering the cause of yellow fever. They contributed to research on vaccinations for typhoid fever, and during World War I, AMM staff were involved in vaccinations and health education campaigns, including major efforts to combat sexually-transmissible diseases.
By World War II, research at the AMM focused increasingly on pathology. In 1946 the AMM became a division of the new Army Institute of Pathology (AIP), which became the Armed Forces Institute of Pathology (AFIP) in 1949. The AMM's library and part of its archives were transferred to the NLM when it was created in 1956. The AMM itself became the Medical Museum of the AFIP in 1949, the Armed Forces Medical Museum in 1974, and finally the NMHM in 1989.