The Church of St Stephen has very ancient origins, dating from the 5th century. But its present form is mainly the result of a long building campaign during the 12th century, recognisable by the typical facing of courses of brick alternating with stone, adapted during the centuries that followed. The church has a typically symbolic cross-shaped floor plan. The set of three naves, supported by round arches, crosses the transept forming an octagonal tiburium (a tower raised over the arms of the cross shape). The entire transept is raised, and contains an oratory crypt (perhaps built as early as the 11th century), characterised by cross vaults on columns. The crypt is accessible from the side aisles. The altar space, enclosed by a semicircular apse, is reached via a staircase from the nave and has two overlapping walkways (ambulatories), one serving the crypt and one the presbytery. This architectural complexity makes St Stephen a unique case in the Romanesque church art of Verona.

One of the main additions to the medieval church was the Chapel of the Innocents, commissioned by parish priest Giulio Varalli between 1618 and 1621. According to tradition, it houses the relics of four children killed in the Massacre of the Innocents ordered by King Herod. The chapel is an example of the Baroque style, and is recognisable (even from the outside) by its dome. The canvases displayed on the three altars among the decorative stuccoes are by the three leading Veronese artists of the period: Pasquale Ottino, Marcantonio Bassetti and Alessandro Turchi, known as Orbetto.