The walls of the nave bear the remains of frescoes with scenes from the Passion of Christ (right) and stories from the life of St. Francis (left), by the so-called Master of St. Francis (circa 1253).
Near the end of the left wall, in a niche above a Gothic dais, is a fresco of the Coronation of the Virgin by Puccio Capanna (14th c.).
In the middle of the nave, a staircase leads down to the crypt; behind the altar is the urn containing the remains of the saint, protected by an iron grate. 
Returning to the church, the Chapel of the Magdalene preserves precious frescoes (from about 1314) depicting stories of Mary Magdalene and the Saints, attributed to the school of Giotto, and perhaps including some painting by the master's hand.
The first chapel on the left displays episodes from the life of Saint Martin, by Simone Martini (1312-1320).
In the vault crossing, above the Gothic altar, are other frescoes attributed to Giotto's assistants, including the Maestro delle Vele (Master of the Assisi vaults).
The walls and the barrel vault of the right transept preserve frescoes by the school of Giotto and a Madonna Enthroned with Angels and St. Francis, a great composition by Cimabue, which has been partially reduced. On the neighbouring wall at the end are five figures of saints, attributed to Simone Martini.
The chapel of St. Nicholas, too, is decorated with frescoes from the school of Giotto (1300 to 1310), possibly executed with assistance from the master himself, and representing stories of that saint.
In a niche above the altar is the Gothic tomb of Giovanni Gaetano Orsini by an unknown Umbrian master.
On the walls and on the vault of the left transept, visitors can admire the cycle of the Passion of Christ and a Madonna and Saints by Pietro Lorenzetti and his workshop (1315-20), among other paintings.

Upper church
If the solemn and dark lower basilica invites penance and silence, the upper church soars into the sky, airy and bright.
In a Gothic style with French influences, the nave has four bays, cross vaulting, and a polygonal transept and apse.
The transept is wonderfully decorated with frescoes by Cimabue, with the famous Crucifixion, scenes of the Apocalypse and Stories of St. Peter. Started in 1277, the cycle has been damaged by changes in which the colour white has taken on a dark tone, giving some images an appearance of photographic negatives.
Cimabue and his assistants also painted the four Evangelists on the ceiling above the Gothic high altar and the frescoes with Stories of Mary on the walls.
In the upper portion of the nave there is a cycle of frescoes with Stories of the New and Old Testament, thought to be partly the work of painters of the Roman school and partly by followers of Cimabue.
The space of the narrative scenes is interspersed with windows adorned with medieval stained glass windows, which, despite the reconstruction, make up one of the most complete such sets in Italy.
The bottom part of the nave walls is decorated with the famous fresco cycle designed by Giotto, who supervised its completion by other hands. The cycle contains scenes from the life of St. Francis, from his youth through death and to posthumous miracles attributed to him, framed by painted architecture depicting columns and brackets.

Museum of the Treasury of the Basilica of St. Francis 
From the first floor of the Renaissance Cloister of Sixtus IV, one enters the Museum of the Treasury, a collection of sacred art that includes paintings, objects in gold and textiles related to the history of the basilica. 
In the adjacent room is the Perkins collection: donated to the city in 1955 by the American art historian Frederik Mason Perkins, it includes panel paintings of the 14th and 15th centuries.

Hours
Winter months (standard time):
upper church 8:30 a.m. – 6:00 p.m. (last entrance 5:45 p.m.),
lower church 6:00 a.m. – 6:00 p.m.
Summer months (daylight savings/summer time):
upper church 8:30 a.m. – 7:00 p.m. (last entrance 6.45 p.m.),
lower church 6:00 a.m. – 7:00 p.m.

Heures