It was for many years an important stop for pilgrims on their journey to Rome or to the Holy Land, because it was said to contain the tomb of the Three Magi or Three Kings.

Probably founded in the 4th century, its name refers to Eustorgius I, the bishop of Milan to whom is attributed the translation of the supposed relics of the Magi to the city from Constantinople in 344.

In 1764, when an ancient pillar was removed, a Christian burial was discovered, housing coins of emperor Constans, the son of Constantine the Great.

Behind the apse is the most striking feature of the church, the Portinari Chapel (1462–1468), one of the most celebrated examples of Renaissance art in Lombardy.

The chapel also houses an important Dominican monument, the Ark (tomb) of Saint Peter of Verona, which is replete with marble bass-relief images by the sculptor, Giovanni di Balduccio.