The osteology collections have evolved through donations or exchanges with other museums or anthropological institutes, also archaeological excavations of burial sites, hill forts (settlements of the Bronze Age and Iron Age) or caves, and exhumations of cemeteries or ossuaries, as well as purchases from hospitals or other agencies and charities.

Some exhibits are datable to the prehistoric or protohistoric era but the majority are from the late 19th century and the early years of the 20th century.

Most of the items are of Italian origin, but there are also many from neighbouring European countries (Germany, Austria, Albania, Greece); some are of African origin (Libya, Egypt, Ethiopia), others from Asia (Central Soviet Asia, Turkey, India, Malaysia, China) and South America (Peru, Bolivia and Paraguay).

The Phrenology Collection — a set of 9 skulls showing signs of natural or induced deformation — is of particular interest as it bears witness to the 19th century pseudoscientific doctrine which suggested that the character of a person could be deduced from the morphological characteristics of the skull.

There is also a faunal collection of Primates: along with six highly prized whole skeletons (Cercopithecus, Pongo, Pan troglodytes and Gorilla), the exhibits include several skulls and other osteological remains both of these same genera and of Cebus, Macac, Papion and Theropithecus.

The key stages in the evolution of our species are documented in an extensive and continuously updated set of fossil casts, used essentially for educational purposes.

Through a particularly important acquisition completed in 2016, remains from Al Khiday (central Sudan) were procured for the museum. These consist of some 200 human skeletons that shed light on customs regarding death and funeral rites in certain ancient societies (from 12,000 BC to the 4th-6th centuries BC), which inhabited an area fundamental to a fuller understanding of the dynamics behind the expansion of Homo sapiens beyond the borders of Africa.

Somewhat on the fringes of the osteology collection, but still concerned with physical Anthropology, is a set of plaster face masks, acquired by Raffaello Battaglia in 1936 from professor Lidio Cipriani of Florence: it comprises around 120 facial casts of individuals belonging to various peoples of Africa (Tuareg, Bari and Kunama, Ethiopian, Zulu, Bushman, Pygmy), Asia (Arab) or the Far East (Chinese).