Francis died at the age of forty-four and already two years later, on July 16th, 1228, his solemn canonization took place in Assisi. On that same day the Pope laid the foundation stone of the future Basilica of Saint Francis, which was to become the Head and Mother of the Franciscan Order. During the first phase of the building works were directed by the Vicar General of St Francis, Friar Elia from Assisi, who had been the ministry general of the Order. On his removal from that office also his activity as organizer and supervisor of the construction came to an end.

What was the original intention like? That is what critics wonder about still nowadays, having been unable to take to a unitary conception the stylistic discordance between the lower part, the so-called Lower Church, and the upper part, that is the Upper Church. They think that the sanctuary must have been conceived since the very beginning as a two-storey church, of which the lower part was to hold the remains of Saint Francis and to become the memorial church. The upper part, instead, was to be the official place for liturgical services: that’s why in its apse there stands the papal throne and the Pope himself is the Bishop of that church.

As already mentioned, the official character of the upper Church as the place for liturgical solemnities is reinforced by the presence of the papal throne in the apse. However, in the architectural structure of the whole building, the lower Church got the typical function of a “crypt”, that is of a mausoleum erected on the sepulchre of a Saint, as in the ancient early Christian churches. Only later, in 1749, under the papacy of Benedetto XIV, also the lower Church was granted the privilege of a second papal throne. For justification’s sake we must say that almost at the very beginning of its existence several chapels were opened on the sides of the crypt. The multiplication of the altars caused also the increase in number of the masses, which very soon exceeded those celebrated in the upper Church.The Sanctuary of Assisi is one of the most ancient gothic churches on the Italian soil; not very long after the building of the basilica had been ended, the pictorial decoration was started. As it was rightly said, “architecture and painting make an inseparable unity”: the frescoes, in fact, conceived since the very beginning, are part of the architecture of the church. From this point of view no other Church can bear comparison with the Basilica of Assisi. The large surfaces of the walls of both churches superimposed seemed to have been created just to keep the pictorial poem that covers the interior of the basilica today.