The present Basilica is mainly the result of three rebuildings which have followed one after the other in the space of around seventy years: 1238 – 1310.

At the time of St Anthony the small Church Santa Maria Mater Domini was here, later on it became a part of the Basilica, corresponding to the Chapel of the Madonna Mora. The Monastery of the Franciscans, probably founded by St Anthony himself in 1229, was close to the small Church. 

After the death of St Anthony  in a monastery of Clarisse nouns in Arcella, a suburb of Padua, in 1231, his body was – according to his wish – deposited in a marble tomb and buried in the Church of Santa Maria Mater Domini.

The first portion of the Basilica, a Franciscan church, with only one nave and short apse, was started in 1238;  two side aisles were added later on, up to the marvelous building we can admire today.