The first stone of the Lower Basilica was laid on July 17th 1228 (by Pope Gregory IX) on the day after the canonisation of St Francis. Two years later the saint's body was brought here in secret for fear of looting by tomb raiders and buried in the unfinished church. It had earlier been resting in the church of San Giorgio (the future church of St Claire's). It is unclear when the work on the Upper Basilica started. It is commonly believed that it must have been after the abdication from the order of Brother Elia in 1239, who had until then directed the works on the Romanesque Lower Basilica. Built in the area of Assisi popularly known in the Middle Ages as the “hill of hell” (as it was used for public executions) the church of St. Francis of Assisi rises up today in the place where the Saint chose to be buried.

Pope Innocent IV consecrated both churches in 1253 the square outside the main facade did not exist at the time and it was also before work started on the large cycle of fresco decorations. A flight of steps led upwards to the gothic entrance, pierced by a large rose window surrounded by the symbols of the four evangelists. A central drum in turn sealed this off. The lateral towers served as supports for the structure, while those near the choir, contained stairs.

1487 saw the addition of another entrance. This one was in front of the old gothic entrance. Francesco da Pietrasanta designed it. Other parts of the cathedral that were built at the same time are the lower square and the oratory of San Bernardino. On the left side of the façade is the benediction loggia, which was added in 1754, the year in which the church was raised to the status of basilica. After this they ran out of space on the hillside and all further constructions had to stretch the cathedral outwards in the opposite direction.

The transept is the first thing you see on entering the Lower Basilica. It was built between 1280 and 1300. A single nave runs through the ceiling of the Lower Basilica. It is supported up to the semicircular apse by cross vaulting. Opposite the entrance are lateral chapels that were added between 1350 and 1400.

In 1818, the crypt that held the remains of St Francis was discovered. This led to its renovation to the designs of Pasquale Belli in 1822. Ugo Tarchi redesigned the crypt in the neo-Romanesque style between 1925 and 1932. Ceccolo di Giovanni painted a fresco, in the 15th century. You can find this on the left hand wall of the entrance transept, next to the chapel of San Sebastiano. Opposite it stands a 14th century gothic funerary monument to the Cerchi family of Florence.

The chapel of St. Catherine of Alexandria was built in 1367 to the design of Gattapone after it was commissioned by Cardinal Albornoz, who was buried here after his death. The transept terminates here. This chapel contains Andrea da Bologna’s frescoes of the life of St Catherine, painted in 1368.

The high altar of the basilica was built in 1230. Above it, a canopy, surrounded by 12 columns, was built in the 14th century, but was removed in 1870. The vaulted is decorated with paintings of St Francis’ Apotheosis and also allegories like Poverty, Chastity and Obedience. On the right hand side of the transept is a series of paintings like the chilhood of Christ and Posthumous Miracles of St Francis. There are partly credited to the workshop of Giotto (1315-20). It also contains work by Cimabue (Enthroned Madonna with Angels and St Francis, 1280), and Simone Martini (1321-26 Madonna with Child and Two Wise me and St Francis, St Ludwig of Toulouse, St Elisabeth of Thuringia, St Claire and an Unknown Saint). The left side of the transept was completely decorated by Lorenzo Lorenzetti and his workshop between 1315 and 1330.

The walls of the apse were earlier had frescoes depiction an allegory of Crucifixion on them. Last Judgement by Cesare Sermei di Orvieto has replaced it now. Apollonio Petrocchi da Ripatransone completed the wooden choir in 1471.

The chapel of St Ludwig of Toulouse and St Stephen had frescoes by Dono Doni, painted in 1575. It also has a Simone Martini stained glass window. After this chapel you will find two more chapels – one built to commemorate St. Anthony of Padua and the other for Mary Magdalene. This latter has a series of frescoes by Giotto and his workshop in 1320.

Pope Sixtus IV asked for a cloister to be built in 1476. Stairs on either side of the choir lead you to it and you can get to the Upper Basilica and the Museo del Tesoro from here. The latter is a must see as it houses relics, valuable manuscripts, vestments and 13th century works. In rooms adjacent to the Museo you can find 14th and 15th century panels collected by Perkins.

The Upper Basilica is built on the original plans for the Lower Basilica, with a single nave with two lateral arms and a polygonal apse. However the Upper Basilica, though unique in style and design, has features of French architecture. It is simple unlike the Lower Basilica with a gallery running around it. Cimabue and his workshop decorated the Upper Basilica in 1280. The only exception is the upper right hand side section, which was decorated by a Gothic and Roman artist between 1267 and 1270. The nave contains 34 episodes from the Old and the New Testament. This work of art is attributed to the painters of the Rome School and the followers of Cimabue. This excludes the scenes from the life of Isaac, which are attributed to Giotto.

The walls under the gallery are decorated with 28 frescoes on the life of St Francis. The Life of St Francis by San Bonaventura inspired these. It is not clear who painted these beautiful frescoes. It is however commonly attributed to Giotto.

A German workshop was commissioned for the stained glass windows of the choir. This was due to the backwardness of the Italian artisans in this form of art. The stained glass windows were the first decorative element to be completed in the church. International help was used again during the construction of the windows on the left hand side of the church. It is believed that a French workshop created this structure.