The stained glass windows of the choir, listed as a historical monument, were created and put up in 1555-1556 by the master glassmaker Nicolas Beaurain.

The Sainte-Chapelle (from 1379) was left unfinished by Charles V and Charles VI and completed by Francis I and Henry II. Philibert de L'Orme managed to copy the original style almost exactly. In 1550 a choir-screen was ordered from the sculptor Jehan de la Gente and choir-stalls (destroyed 1789-1799) to house 84 canons and choristers were commissioned from Francisque de Carpy (active ca. 1531-1558). On either side of the sanctuary are the private chapels of the king and queen, each with a fireplace. The Queen's Chapel contains the monument to Louis Antoine Henri de Bourbon, Prince Conde, Duc d'Enghien (marble, 1816-1822) by Louis-Pierre Deseine.