It is one of the first convents of the Order of Friars Minor. The small church seems to date back to the seventh or eighth century. Some documents, however, place it at 1030, stressing that it was the property of the bishops of Assisi and that - at least until 1198 - it was guarded by a secular priest.
It rises where St. Francis prayed and heard the voice of the crucifix who called him by name and said: "Go and repair my house that is about to fall". The Saint obeyed that invitation and set his hand to reconstruction. Also here, between 1211 and 1212, Clare founded an order of cloistered.
Next to the church there was a building with a large dormitory, 22x8 meters long: it is a bare and unadorned room in which the first sisters took their rest, lying on straw beds. At the bottom of this place is the door from which, on June 22, 1234, St. Clare faced with the SS. Crucifix to remove the Saracens. Perhaps already in sec. XII, the "Church of S. Damiano" had the current proportions. There was the whole block of buildings that constitute the "historical" part of the Sanctuary: the "Coretto di S. Chiara", the "Sacristy", the "Sepulchre" (where the first nuns were buried), the "Dormitory of the Saint", the "Infirmary" the "Inner Oratory", the "Garden of the Canticle".
The other parts were added from sec. XVI.
The convent of San Damiano was enlarged in 1504; in 1517 the chapel of San Girolamo was built - with a valuable fresco of Tiberius of Assisi - overlooking the church's facade.
In 1535 a new chapel was built to house the "miraculous" crucifix by Fra Innocenzo da Palermo.
The sacristy, all in worked walnut, is equipped with wardrobes, credenze and bulkhead. In front of the sacristy there is the choir, where the first community of nuns gathered for common prayer. On the ground floor, there is a cloister - from here, it is possible to access the refectory of St. Clare, in which the nuns consumed their meals. The convent has a library and several working rooms; the perimeter of the cloister is about 520 meters.