At the end of the 3rd century AD, in the south eastern area of the Roman town, the area now occupied by the Basilica and its surrounding land, there was the trade centre with warehouses, markets and homes. On this site in the year 313 Theodore started to built the first church. It was made up of two large rectangular halls. They were parallel to each other and connected horizontally by a third hall, that was flanked by smaller rooms such as the Baptistery with a round baptismal font. 
The Theodorian building was radically changed around the first half of the IV Century by one of the successor bishops, probably Fortunaziano, this alteration was carned out by reason of the changed liturgical purposes. The remains of the Post-Theodorian north hall are visible in the excavated crypt.
In the IX century the patriarch Massenzio took a definitive restoration which changed the entire aspect of the building. The transept which gave the Basilica a cross shaped plan for the first time, and the crypt under the presbytery were the main examples of the patriarch's work. Then he has the facade of the Basilica adjusted building the porch, and he also restored the Baptismal font and linked it to the Basilica through the, so called, Pagan's Church. 
After more or less two centuries in the first half of the XI century, the Patriarch Poppone thought it necessary to carry out further restoration. He raised the parametre walls, made a new root, and the apse was completely frescoed with images of great monumentality and with classic style decorations of Roman inspiration. Poppone raised the bell tower which dominates plain of Friuli.
In the second half of the XII century, the Patriarch Voldorico of Treffen embellished the Massential crypt with a series of frescoes. It is the biggest Romanic-Gothic pictorial series of the region and one of the most important in Northern Italy.

From the Middle Age to the 19th century the Basilica had more additions of lesser importance such as the Chapel called "dei Torriani", the Chapel of St. Peter, the Chapel of the Holy Almighty or of St. Ilario and the Chapel of the Rosary. Also there is the sarcophagus of the 14th century probably being the work of Filippo de Sanctis and the Holy Sepulchre.