The most famous features of the chapel, among the finest of their type in the world, are the great stained glass windows, for whose benefit the stone wall surface is reduced to little more than a delicate framework. Fifteen huge mid-13th century windows fill the nave and apse, while a large rose window with Flamboyant tracery (added to the upper chapel c.1490) dominates the western wall.

Much of the chapel as it appears today is a re-creation, although nearly two-thirds of the windows are authentic. The chapel suffered its most grievous destruction in the late eighteenth century during the French Revolution, when the steeple and baldachin were removed, the relics dispersed (although some survive as the "relics of Sainte-Chapelle" at Notre Dame de Paris)