The villa was built by Ferdinando I in 1587, probably on a design by Bernardo Buontalenti who erected it on the foundations of a pre-existing palazzo. Its imposing mass is characterised by four corner towers which make it a villa-fort. Situated in the vicinity of the confluence of the Pesa and Arno rivers, it was a resting place for transfers of the Court between Florence and Pisa, as well as serving as a grand-ducal hunting lodge. Also noteworthy is the garden, embellished by scenographic giochi d’acqua.

It was here at the Medici Villa l’Ambrogiana that in March and April, 1681, the great scientist from Arezzo Francesco Redi studied the genital apparatus of female hares, performing numerous dissections. Particularly important from the viewpoint of historical-scientific iconography is the collection of paintings with a botanical and zoological subject that Grand Duke Cosimo III de’ Medici commissioned from Andrea Scacciati and Bartolomeo Bimbi to embellish the villa.

Towards the mid 19th century, after more than two centuries of glorious history, Grand Duke Leopold II converted it into a home for the mentally ill. It was then a prison for women and minors, and in 1886 it was decided to make it the Mental Asylum for the Criminally Insane. The building is therefore not accessible, though in several periods of the year, guided tours are organised to allow visitors to admire several rooms, the cloister, chapel and garden. A fine city park unfolds outside the villa walls.