The basilica isn't one church but two, the Gothic upper part built a scant half century after the Romanesque lower one. Work on this two-tiered monolith was begun a few years after the death of St. Francis. His coffin, unearthed from its secret hiding place after a 52-day search in 1818, is on display in the crypt below the Lower Basilica. Both churches are magnificently decorated artistic treasure-houses, covered floor to ceiling with some of Europe's finest frescoes: the Lower Basilica is dim and full of candlelight shadows, while the Upper Basilica is bright and airy.
The first chapel to the left of the nave in the Lower Church was decorated by the Sienese master Simone Martini (1284–1344). Dating 1322–26, the frescoes show the life of St. Martin—the sharing of his cloak with the poor man, the saint's knighthood, and his death. There's some dispute about the paintings in the third chapel on the right, which depict the life of Mary Magdalen. Experts have argued for years,
with many attributing them to Giotto (1266–1337). There's a similar dispute about the works above the high altar, depicting the marriage of St. Francis to Poverty, Chastity, and Obedience—some say they're by Giotto; others claim them for an anonymous pupil. In the right transept are frescoes by Cimabue (circa 1240–1302), including a Madonna and saints, one of them St. Francis himself. In the left transept are some of the best-known works of the Sienese painter Pietro Lorenzetti (circa 1280–1348). They depict the Madonna with Sts. John and Francis, the Crucifixion, and the Descent from the Cross.
It's quite a contrast to climb the steps next to the altar and emerge into the bright sunlight and airy grace of the double-arched Renaissance Chiostro dei Morti (Cloister of the Dead). A door to the right leads to the Tesoro (Treasury) of the church and contains relics of St. Francis and other holy objects associated with the order.
In the Upper Church the frescoes show that Giotto, only in his twenties when he painted them, was a pivotal artist in the development of Western painting, breaking away from the stiff, unnatural styles of earlier generations and moving toward realism and three-dimensionality. The paintings are meant to be viewed from left to right, starting next to the transept. The most beloved of the scenes is probably St. Francis Preaching to the Birds, a touching painting that seems to sum up the saint's gentle spirit. In the scene of the dream of Innocent III (circa 1160–1216), the pope dreams of a humble monk who will steady the church; in the panel next to the sleeping pope, you see a strong Francis supporting a church that seems to be on the verge of tumbling down—a scene that resonates with irony today. The dress code here is strictly enforced—no bare shoulders or bare knees.