Under S. Peter's basilica is an important necropolis composed by brick mausoleums arranged along a funerary way. The oldest ones are on the line to the north of the way, dating back to the II century AD, those of the south side, the latest ones, date back to the III century AD. The sepulchres have inscriptions with the names of the dead and are frescoed and stuccoed inside; some of them have white and black mosaic floors. Interesting the inscription on the mausoleum of Popilius Heracla, quoting a part of his will where the deceased required his heirs to bury him "in the Vatican near the arena"; this is a precious topographic indication to locate Caligula's arena, near the Vatican necropolis.

Another important sepulchre is that of the Iulii, whose frescoes depict Christian themes such as Jonah in the jaws of a whale and the Good Shepherd, while in the vault is a mosaic depicting Jesus Christ riding the Sun's chariot, like the pagan god Apollo.

Afterwards, the space of the necropolis was occupied by other tombs, even though the major part of the Christian sepulchres were in the western part, where is a small rectangular square surrounded by mausoleums built around what was identified as Peter's tomb, near the arena where the apostle was martyred. This was in the origin a simple hole; around the middle of the II century AD, a monument was built upon the tomb, leaning against a wall, whose entrance was from two stairs to the south. This monument was formed by a niche with two pillars supporting a covering slab of travertine upon which was a smaller niche. Underneath, another underground niche contained the tomb of Peter, as proven by a graffito on the wall behind the biggest niche, where you can read the name of the apostle in Greek letters.

In the IV century the basilica was built by Constantine upon the tomb of Peter. Began around 320 AD it was consecrated in 326 by Pope Sylvester I and realized in 349. The church with a nave and double aisles divided by pillars had a colonnaded atrium and was closed by an apse separated from the aisle by a transept, in the centre of which was the funeral monument of Peter. On top of the sepulchre was a shrine placed in the centre of the presbytery, on top of the shrine was a canopy supported by four spiral columns portraying putti gathering grapes. Two more columns were behind the apse. The Constantine basilica had no altar, since it was not for liturgy but for funerary use. Only afterwards, in the IV century, to practice the liturgy and protect the sepulchre was raised the floor of the presbytery, in front of which was added a double row of six spiral columns, the innermost of them was closed by plutei. The sepulchre of Peter was accessible via two side steps. Eleven of these columns are still in the present basilica of St. Peter. The Constantine basilica was intact until the XV century, when Pope Nicholas V (1447-1455) decided the rebuilding of the edifice due to its precarious conditions.