The museum is home to one of the largest collections of cetacean skeletons in Europe, showcasing an impressive array of marine mammal specimens.

In addition to its extensive cetacean holdings, the museum's oldest collections include seashells amassed by the Italian invertebrate scientist, Niccolò Gualtieri.

Serving as both an educational and research institution, the museum invites visitors and scholars to explore the diversity and complexity of the natural world.

The collection is a remarkable example of the fusion between science and craftsmanship.A project to devote the garden to the plants of Monte Pisano is currently underway.

When the friars still inhabited the Certosa, it was used for drying hay and grains, which were then stored in the numerous silos located at the edge of the structure.

The exhibition was organized in 2018 into eight thematic areas containing more than 28 skeletons from the 27 species present in the collection, as well as 11 life-sized models including a baleen, five casts of fossils mostly discovered and studied by the team of the University of Pisa, such as that of Livyatan melvillei as well as from real fossils, such as the holotypes of Balaenula astensis, found in Portacomaro in 1940.

However, a large part of them was donated to the Museum by the Florentine paleontologist Roberto Lawley, such as an individual's remains from Etruridelphis giulii.

The biblical myth is contested by descriptive panels, samples of volcanic rocks, and explanations of Earth's origin through evolution.

In 1814, the University of Pisa decided to separate the chairs of scientific teaching, entrusting Gaetano Savi with that of Botany and Giorgio Santi that of zoology, paleontology and geology.

This separation of the chairs meant that the museum, which also included the botanical collections under a single direction, was divided into two distinct administrations with greater decision-making autonomy.

Savi called upon the Neapolitan Leopoldo Pilla to fill the museum and this brought a large number of Vesuvian rocks and crystals with him.