The sanctuary is dedicated to the figure of Saint Margaret, patroness of Cortona and Franciscan tertiary, and to the subsequent cultural and spiritual activity of the Observant Franciscans. Upon the death of the saint (22nd February 1297) it was decided to build a church in her honour, next to the ancient little church of San Basilio that Margaret herself had restored after choosing it as a place of penitence and prayer. In 1304 the sacred building was already built, but it continued to be embellished with important frescoes throughout the fourteenth century. Only a few fragments of this mural cycle have come down to us, preserved in the Diocesan Museum, but there is evidence of it in a 17th century codex that documents with twenty-one watercolour scenes the mural paintings lost in 1653 when, due to their poor state of preservation, they were faded out. Analysis of the surviving fragments leads us to date them to around 1335 and attribute them to the workshop of one or both of the Lorenzetti brothers. In 1385 the church was entrusted to the Olivetan monks, who were replaced in 1389 by the Minor Observants who still take care of it today and welcome visitors. In August 1927 it was elevated to the dignity of a minor basilica.
