The Villa Medici lies within the historic district of Rome, inside the perimeter walls built by Emperor Aurelian in the third century, and the Gianicolense walls built by Pope Urban VIII in 1643, which was declared a World Heritage Site by the United Nations Educational, Scientific and Cultural Organization (UNESCO) in 1980, though it is not specifically identified amongst the mostly Roman-era monuments of that listing, and it is not part of the UNESCO World Heritage Site the "Medici Villas and Gardens in Tuscany," ascribed in 2013.

The sole dwelling was the Casina of Cardinale Marcello Crescenzi, who had maintained a vineyard here and had begun improvements to the villa under the direction of the Florentine Nanni Lippi, who had died however before work had proceeded far.

The new proprietors commissioned Annibale Lippi, the late architect's son, to continue work, with involvement of Michelangelo that is traditional lore, but undocumented.

Under the Cardinal's insistence, Ammanati incorporated into the design Roman bas-reliefs and statues that were coming to sight with almost every spadeful of earth, with the result that the facades of the Villa Medici, as it now was, became a virtual open-air museum.

These two rooms were only uncovered in 1985 by the restorer Geraldine Albers: the concealing whitewash had protected and conserved the superb fresco decoration carried out by Jacopo Zucchi in 1576 and 1577.

When the Cardinal succeeded as Grand Duke of Tuscany in 1587, his elder brother having died, he satisfied himself with plaster copies of his Niobe Group, in full knowledge of the prestige that accrued to the Medici by keeping such a magnificent collection in the European city whose significance far surpassed that of their capital.

For a century and a half the Villa Medici was one of the most elegant and worldly settings in Rome, the seat of the Grand Dukes' embassy to the Holy See.

Subsequently, it housed the winners of the prestigious Prix de Rome, under distinguished directors including Ingres and Balthus, until the prize was withdrawn in 1968.

The Académie des Beaux-Arts in Paris and the Institut de France then lost their guardianship of the Villa Medici to the Ministry of Culture and the French State.

[7] Work continued under the direction of the previous director, Richard Peduzzi, and the Villa Medici resumed organizing exhibitions and shows created by its artists in residence.

The Academy continues its programme of inviting young artists, who receive a stipend to spend twelve months in Rome, exhibiting their work.