The Warren Anatomical Museum originated from John Collins Warren's (1778-1856) donation of his personal teaching and research collection. Like many of his medical peers, Warren collected anatomical and pathological preparations to aid his practice and study. His collecting began as early as 1799, and he gradually expanded his collection to help teach his medical students. When Warren resigned his Harvard professorship in 1847, he presented most of his collection to the University with an endowment of $5,000 to support its preservation.
The Warren Museum became one of this country's leading medical museums and physicians such as Oliver Wendell Holmes, Sr., first Warren curator J. B. S. Jackson, Henry Jacob Bigelow, J. Collins Warren and others contributed anatomical specimens and models, instrumentation and medical memorabilia to its holdings. During the 19th and early 20th century, the museum's collection of both normal and pathological specimens served as an important resource for the study and teaching of medicine at Harvard Medical School. In 1888 John Shaw Billings called the Warren Museum "the best museum associated with a medical school in this country" in his Medical Museums with special reference to the Army Medical Museum at Washington. When the museum opened for study in 1847, it was housed in a large room on North Grove Street in Boston. It was here, in 1861, that the collection was first opened to the public. In 1883, the Museum moved with the Medical School to Boylston Street, and again in 1906, to the Longwood campus, where it occupied the upper floors of Gordon Hall until 1998. In 2000, the Countway Library's Center for the History of Medicine took over curatorial responsibility for the Museum and created exhibit space for part of the collection on the Library's fifth floor.