The confessio, located before the main altar, was built by Luca Carimini from 1869 to 1871 during excavations which uncovered the original crypt. The remains of this show it to have had a U-shaped plan. At the nave end was a small aisled hall, with three pillars on each side. At the curved end were two staircases leading down from the main church, and wrapped round the curve was an ambulatory or passage through which pilgrims could file to venerate the shrine of the two apostles which was in a little cubicle halfway along.

The wall frescoes are reproductions of catacomb paintings, apparently inspired by those to be found in the Catacombs of Domitilla, and executed 1876-1877. This is because, as well as the original relics of the apostles, other saints' relics were preserved here when they were taken from the catacombs in the 9th century to protect them from invaders. An inscription explains that one of those who helped move these relics was Pope Stephen IV. Unfortunately, damp has been damaging these frescoes.