Later in the 13th century, the aisles were added in a more Gothic style, the length of each nave bay being divided into two aisle bays with pointed arches and quadripartite vaults.

The eastern apse was also extended in the Gothic style, receiving a ribbed vault and nine radiating chapels in the French manner. Later also, the Treasury chapel was built in 1691 in the Baroque style by Filippo Parodi, a pupil of Bernini.

Externally, the brick facade has a Romanesque central section which was extended outwards when the aisles were built, acquiring in the process four deep Gothic recesses and an elegant arcaded balcony which stretches across the broad front of the building. The facade gable shows little differentiation between the nave and aisle, screening the very large buttresses that have the same profile and form a richly sculptural feature when the building is viewed from the side.

The domes, like the domes of St. Mark's Basilica, were raised in height externally, giving a Byzantine appearance to the building, while the multitude of small belfries which accompany the domes recall Turkish minarets. Externally, at the main roof line each section of the building is marked by a low gable decorated with blind arcading in brick. These gables combine with the domes, the broad buttresses and the little towers to create a massive sculptural form, both diverse and unified in its conglomeration of features. As a work of architecture the building is particularly effective when viewed from the north west, an extra dimension being added to the facade by the huge plinth and dynamic equestrian monument of the Condottiero Gattamelata by Donatello.

Art works and treasures

The interior of the church contains numerous funerary monuments, some of noteworthy artistic value. The Chapel of the Holy Sacrament (Cappella del Santissimo Sacramento, also known as Cappella Gattamelata), in the right aisle, houses the tomb of the famous condottiero Gattamelata and of his son Giannantonio. The bronze tabernacle is made by Girolamo Campagna. This chapel, with its broad bands of polychrome and carved Gothic details, has had many stages of decoration, the final stage being the creation of an atmospheric mosaic in the tall rear niche representing the Holy Spirit with rays of golden light descending against a background of intensely blue sky. This highly theatrical work was created by Lodovico Pogliaghi between 1927–36.

Relics of St Anthony are to be found in the ornate baroque Treasury Chapel (begun in 1691). The body of the saint, which was in the Madonna Mora Chapel, has, from 1350, lain in a separate transept chapel, the Chapel of St Anthony, the interior decoration being attributed to Tullio Lombardo, who also provided the sixth and seventh reliefs depicting the miracles of St Anthony (Miracle of the stingy man's heart, Miracle of the repentant man). The third relief Saint bringing back to life a man who had been murdered is a masterpiece by Girolamo Campagna. The late-16th century statues are by Tiziano Aspetti

The Basilica contains several important images of the Madonna. The Madonna Mora is a statue of the Madonna with the Christ Child by the French sculptor Rainaldino di Puy-l'Evéque, dating from 1396. Her name refers to her black hair and olive skin tone, being interpreted as "swarthy".

The Madonna del Pilastro is a mid-14th-century fresco by Stefano da Ferrara, located on the pier adjacent the left aisle.

Among other sculptural work is the magnificent Easter candelabrum in the apse, finished in 1515 by Andrea Briosco and considered his masterwork. The most famous and striking features of the high altar area are however the bronze Madonna with Child and six statues of Saints by Donatello, who also executed four reliefs with episodes of life of St. Anthony.

To the right hand side of the nave, opposite the tomb of the Saint is the large Chapel of St. James, commissioned by Bonifacio Lupi in the 1370s in the elegant Gothic style, with frescoed walls depicting the Stories of St. James and the Crucifixion by Altichiero da Zevio. Altichiero's Crucifixion is one of the most significant paintings of the late 14th century. There are several frescoes created by Girolamo Tessari.