In 1145, in Via Brolo, Milan, a hospital was built near the Santo Stefano Maggiore Church.

The graveyard, filling with bodies from the new hospital, soon proved insufficient. Not long after, in 1210, a little chamber was built to collect the bones from the hospital, and, in 1269, another small church was constructed near the bone chamber.

(And in 1738, King John V of Portugal was so affected by the sight of the Chapel that he decided to built an exact copy of it in Evora, near Lisbon.)

Today, the ossuary at San Bernardino alle Ossa is located at the end of a short corridor to the the right of the church's entrance. The vault is decorated with frescos from Sebastiano Ricci, dating from 1695. The building's walls are completely covered in bones and skulls, some from the old ossuary, some from other local graveyards; they also decorate the doors and the pillars.

Some have speculated that the bones belonged to martyrs killed by heretics in St. Ambros' time. The bones, however, mostly seem to have come from the patients of the ancient Ospedale del Brolo (the local hospital), from monks that operated the hospital, and from people who died in prison.