The Museum is located in the convent of Santa Caterina da Genova, in the historic district of Portoria, and its entrance corresponds to the one of the place once known as the Deposito di Santa Caterina. The building's history is directly tied to that of the old Ospedale di Pammatone, which stood just next door. The hospital began its activity in 1422, when Genoese notary Bartolomeo Bosco purchased three old houses in Vico Pammatone for the creation of a women's hospital. At the beginning of the 20th century, the hospital was transferred to the site of San Martino. For several decades the former hospital building housed various university faculties, and in the Second World War it was damaged during the bombings of 1941-43. After undergoing major renovation work between 1966 and 1974, it became what is now the Palazzo di Giustizia. Inside, it still retains the 18th-century courtyard, the colonnade, the main staircase, and numerous statues of the benefactors of the old hospital.

The convent in which the museum is located was founded in 1488 by Blessed Angelo di Chivasso and, starting from around 1530 and apart from short pauses, it was occupied by the Friars Minor Capuchin, who gave spiritual support to the sick in the nearby di Pammatone and Incurabili hospitals.

The Pammatone area, also known as “dell’Olivella”, is at short distance from the Acquasola esplanade, where the park created in 1835 by architect Carlo Barabino stands today. Interestingly, this esplanade, which stands on part of the old 14th-century walls, opposite the New Walls built by Andrea Doria in 1500, was used in the mid-1600s as a dumping ground for rubble produced in the construction of the Strada Nuova or Via Aurea, today's Via Garibaldi. During the plague of 1657, the area where the park would later stand – and which was already being used as a playground for the game of pall-mall – was used as a mass grave to bury victims of the disease. Still today, these remains lie just a few metres beneath the surface of the road in a kind of underground necropolis. It is said that Columbus’ father lived In the Porta dell’Olivella area and was keeper of the gate.