Near the tomb, below the steps leading up to the chancel, is a room housing some 6th-century ruins that were excavated in 1947-49. These include part of the apse and the , which early pilgrims visited after the tomb of St. Lawrence. In the 9th century it was expanded into an underground chapel with an apse. The shrine is decorated with frescoes that probably date from the time of Pope John VII (705-07), depicting surrounded by saints holding up crowns. More frescoes were added in the 9th century, depicting the Virgin and Child Enthroned accompanied by angels, St. Lawrence, St. Andrew, St. John the Evangelist, and St. Catherine.
The side aisles of the basilica have been uncovered down to original floor level (2.15m lower than the nave) and can be entered via stairs at the front of the nave aisles. The 6th-century aisles provide access to the inner narthex of the same date, which now houses the and is decorated with 19th-century mosaics. The pope's preserved body is on display against the east wall. On the opposite wall, against the structure housing the tomb of St. Lawrence, is the "," a marble slab with a large stain. According to tradition, Lawrence's body was laid on this stone after his execution, staining it with blood.