At the end of the 16th century, the area in front of the Baths of Diocletian was taken up by the Villa Peretti Montalto, one of the most famous of Rome's villas. Built by Domenico Fontana, the architect who worked for Cardinal Felice Peretti-later to become known as Pope Sixtus V- the villa was acquired by the Massimo family at the end of the 18th century.

The building of the railroad and the station entailed the destruction of so much of the villa that the owner Massimiliano Massimo, a Jesuit priest, decided to use the rest of his land to build a Jesuit college.
The imposing edifice, completed in the style of the late Renaissance, continued as the college until 1960 when it became today's museum. Since then, it has housed one of the most prestigious archeological collections in the world.