Set up following mainly prehistoric excavations carried out in the second half of the last century within the framework of a clearly evolutionist perspective which adapted well to the idea of progress sustained by the positivist ideology of the time, it was inaugurated in 1871 thanks to the enlightened work of its first director, Carlo Boni. 

The archaeological collections, arranged chronologically and topographically, are composed of works from an advanced moment in the inferior Palaeolithic period to the Middle Ages. 

Particularly significant are the prehistoric findings, above all the Neolithic ones of Fiorano and Pescale (5th-4th millennium B.C.) originating from the excavations of F. Malavolti, and those of the terramare inhabitants of the Bronze Age - which represent the fundamental nucleus of the museum - with numerous ceramic, bronze and deer-horn objects. 

The ethnological section, set up between 1875 and the early decades of XX century, is composed of findings of different geographical areas, which in many cases bear testimony to by now extinct or dying out cultures. The current arrangement of the collections respects the original 19th century division in geographical areas: New Guinea, South America, pre-Columbian Perù, Africa and Asia.