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The construction of the basilica of St. Francis began immediately after his canonization in 1228. The head of the Franciscan Order has prepared a project for the giant Monastery Sacro Convento, which should surround the Basilica. The Sacro Convento monastery became the spiritual center of the order, although the seat of its head is in Rome. 

After his death, St. Francis was buried in the monastery of St. George, which is now called the Basilica of St. Clare. According to its charter, the Franciscan Order could not own property or land. The land for the construction of the basilica was donated to the Vatican by a resident of Assisi, Simon di Pucarello, and Pope Gregory IX personally laid the first stone at the beginning of the construction of the Basilica of St. Francis. 

The hill where the construction of the Basilica of St. Francis and the Sacro Convento monastery began was called the Hill of Hell, since criminals were executed here. It was immediately renamed the Hill of Paradise, and the head of the Franciscan order, Elijah di Corton, prepared a large-scale project. The walls of the monastery descend along the hill. They resemble the arches of a Roman aqueduct. 

Elijah di Corton had extensive experience in the construction of funerary structures for crusaders in the Holy Land. In the center of the Sacro Convento monastery is located the Basilica of St. Francis. His body is buried in the crypt of the Lower Church. It is located underground. Above the ground rises the Upper Church. Its construction was completed in 1253. 

The Basilica of St. Francis is surrounded by the buildings of the Sacro Convento monastery. Here are the refectory, dormitorium (cells of monks), chapel and rooms for the Pope. In the Middle Ages, the library and scriptorium of the Monastery Sacro Convento was one of the largest in Western Europe, along with Avignon and Sorbonne. 

By the 15th century, the premises for the Pope were greatly expanded and the Popes used the Sacro Convento Monastery as their summer residence. At present, Sacro Convento is no longer a monastery. Since 1971, the Theological University has been located in its premises.