Established in the second decade of the 19th century as the Cabinet of Natural History, the museum actually has even deeper roots, as the first collection of natural history specimens to arrive at the University of Modena dates back to the bequest of the Bishop of Modena Giuseppe Maria Fogliani (1786) of his own collection to the Rectorate.

The most significant portion of the museum's heritage, however, was formed in the second half of the 19th century thanks to some important donations. The exhibition mainly showcases animal fossils, both vertebrates and invertebrates, but there is no shortage of plant remains.

The museum is spread across three locations: the main location of the Department, on Via dell'Università, houses the collections of invertebrate and fossil plants, as well as educational and research activities; in Via Berengario 14, formerly the site of the Anatomy Museum, are housed the Dinosaur Hall and the collections of vertebrate fossils; while in the Foro Boario is the site for setting up the Department's exhibitions.

Evidence from the formations of the Neogene in the Tuscan-Emilian Apennines represents the most substantial segment of the heritage and is due to the research activity of several professors of paleontology at the University of Modena and naturalists of the caliber of Pietro Doderlein and Dante Pantanelli. Among these, for their interest, the remains of marine reptiles from the Cretaceous and Mesozoic deserve mention.

Part of the skeleton of a fin whale recovered about thirty years ago completes the series of local fossils of pelagic origin. In 1926 the museum acquired the Coppi malacological collection, with specimens also originating from the Modenese Apennines. In 1946 the Bentivoglio fossils arrived (plants from the Upper Carboniferous) and later the Montanaro Gallitelli collections (fossils from all over the world).

In the 1960s, skeletons of a Camptosaurus and an Allosaurus from the Utah deposits were acquired, which, along with a perfectly preserved Lower Jurassic Ichthyosaurus (Western Germany) donated by the Ligabue Foundation, are displayed in the "Dinosaur Hall."

Also noteworthy is the collection of ocean fish and fossil palms originating from the famous Bolca deposit, in the Veronese territory. The collections of microfossils are also very rich, in particular, the Di Napoli collection, one of the founders of the modern discipline of micropaleontology.