One of the most popular pilgrimage sites in Christendom combines homage to eternally popular St. Francis, masterworks of medieval architecture, and some of the favorite works of Western art. The basilica is actually two churches, lower and upper; the lower church is dark and somber, a place of contemplation, while the upper church soars into Gothic vaults and is light-filled and colorful, instilling a sense of celebration. This assemblage was begun soon after the saint’s death in 1226, under the guidance of Francis’s savvy and worldly colleague, Brother Elias. The lower church was completed in 1230, and the upper church in 1280. The steeply sloping site just outside the city walls was until then used for executions and known as the Hill of Hell. The presence of the patron saint of Italy, in spirit as well as in body, now makes this one of Italy’s most uplifting sights. His kindness, summed up in his saying, “For it is in giving that we receive,” seems to permeate the soft gray stones, and the frescoed spaces move the devout to tears and art lovers to fits of near-religious ecstasy.

The Lower Church -- Entered off Piazza Inferiore di San Francesco (the lower of the two squares abutting the church), the basilica’s bottom half is a cryptlike church that is indeed, first and foremost a crypt, housing the stone sarcophagus of St. Francis, surrounded by four of his disciples. An almost steady stream of faithful files past the monument, many on their knees. Inside is the saint’s remarkably intact skeleton. Most saints of the Middle Ages fell victim to the purveyors of relics, who made enormous profit dispensing bones, a finger here, a toe there. It’s said that Brother Elias, Francis’ savvy colleague, had the foresight to seal the coffin in stone, and it remained undetected until 1818. The dimly lit atmosphere is greatly enlivened with the presence of many rich frescoes, including Simone Martini’s action-packed depictions of the life of St. Martin in the Cappella di San Martino (1322–1326). Martini amply displays his flare for boldly patterned fabrics and his familiarity with detailed manuscript illumination (many examples would have passed through his native Siena, on the pilgrimage route from northern Europe to Rome). He was also, like Martin, a knight, and these influences show up in several richly detailed scenes, including those of the saint, a Roman soldier, ripping his cloak to share it with a beggar; being investitured; and renouncing chivalry and weaponry in favor of doing good deeds. The imagery is not out of keeping with Francis, who as a youth dreamed of being a soldier.

Giotto and his assistants frescoed the Cappella della Santa Maria Maddalena, with the “Life of St. Mary Magdalene” (1303–1309). An incredibly moving cycle of “Christ’s Passion” (1316–1319) by Pietro Lorenzetti includes a hauntingly humane “Deposition,” in which the young Sienese artist imparts his scene with a gaunt Christ and sorrowful Mary with naturalism and emotion not before seen in painting.

The Upper Church -- Entering the light-filled Gothic interior of the Upper Church, you’ll first encounter scenes of the New Testament by Cimabue, the last great painter of the Byzantine style; some critics say only the “Crucifixion” (1277) is his, and the rest of the scenes are by his assistants. In any case, it’s rather ironic he’s here at all. The artist was infamous for his stubbornness and difficult personality, and in the “Divine Comedy,” Dante places him in Purgatory among the proud, adding the comment, “Cimabue thought to hold the field of painting, and now Giotto hath the cry.” It’s Giotto who famously holds court in the church, with his 28-part fresco cycle on “The Life of St. Francis,” completed in the 1290s. Even nonreligious viewers know and love these scenes of the saint removing his clothing to renounce material processions, marrying poverty (symbolized by a woman in rags), and preaching to the birds (the perennial favorite and the subject of ubiquitous postcards for sale around town).