It is the most important museum in its kind in Italy and includes about 300,000 examples of animal and vegetable fossils, fossil imprints and rock specimens. The initial paleonthologic and geological collections started to be put together by the Medici Grand Dukes and were further increased by the Lorraine family. They were moved to the present day location only in 1925.

Enriched by donations and recent discoveries, the collections include several extraordinary examples. In addition to the lavish collection of Villafranchian mammals from the upper Valdarno (with impressing Proboscidea) there are also: the anthropoid monkey from Maremma (Oreopithecus bambolii), the imprints of mesozoic reptiles from Monte Pisano and non-flying birds (Moa) from New Zealand.

A whole room is dedicated to the evolution of horses; some display stands and panels illustrate the paleonthobiogeography of the Mediterranean region - and in particular of Italy - during the upper Miocene, the theses on the origin of life and the evolution of vertebrates and in particular of Primates.

Besides displaying vertebrates, the museum also offers a wide collection of invertebrates and plants that have been arranged in chronological order in the central gallery of the Museum. The Museum organises didactic activities, guided tours, lessons and temporary exhibitions.