What you can find inside is a great wonder.
Within the Cathedral are two main chapels, a reliquary and tomb. The

Upper Chapel contains beautiful 13th century stained glass and numerous frescos. Unfortunately, many of the frescos (designed by Cimabue and Giotto) were severely damaged in the earthquake of 1997.
The lower section of the wall depicts the life of St. Francis while the upper section has scenes from the Bible. Within the domes you can see the doctors of the church and the four evangelists.

The back of the Cathedral holds scenes of trauma (Christ's death and the Apocalypse) created by Giotto. The Lower Chapel leads to the tomb of St. Francis and his followers. The tomb was built by Francis' disciples immediately after his death. The frescos in the lower chapel are gorgeous, but the lack of light makes the colors and details a bit more difficult to view. You can also enter the reliquary where objects and clothing believed to have belonged to St. Francis.
The entire Basilica is something to experience, whether or not you are a religious individual. The artistry of the building makes it worth a visit.