This was probably the first time that an altar was placed over the tomb of Saint Paul, which remained untouched, but largely underground given Leo's newly elevated floor levels.

Consequently, Pope John VIII (872–882) fortified the basilica, the monastery, and the dwellings of the peasantry,[2] forming the town of Johannispolis (Italian: Giovannipoli) which existed until 1348, when an earthquake totally destroyed it.

[4] On 15 July 1823, a workman repairing the copper gutters of the roof started a fire that led to the near-total destruction of this basilica, which, alone among all the churches of Rome, had preserved much of its original character for 1435 years.

A few months later, he issued orders that the basilica be rebuilt exactly as it had been when new in the fourth century, though he also stipulated that precious elements from later periods, such as the medieval mosaics and tabernacle, also be repaired and retained.

Poletti also asked the scientist Angelo Secchi to design an automatic fire detection and extinguishing system, which was later removed.

Muhammad Ali Pasha, Viceroy of Egypt gave columns of alabaster, while the Emperor of Russia donated precious malachite and lapis lazuli that was used on some of the altar fronts.

On 23 April 1891, an explosion at the gunpowder magazine at Forte Portuense destroyed the basilica's stained glass windows.

The 5th-century mosaics of the triumphal arch are original (but also heavily reworked): an inscription in the lower section attest they were done at the time of Leo I, paid by Galla Placidia.

The subject portrays the Apocalypse of John, with the bust of Christ in the middle flanked by the 24 Doctors of the Church, surmounted by the flying symbols of the four Evangelists.

The nave's interior walls were also redecorated with painted scenes from Saint Paul's life placed between the windows of the clerestory.

Outside the Basilica is the original sculpture of When I was in Prison, created by Canadian artist Timothy Schmalz as part of the Matthew 25 collection installed throughout Rome on the occasion of the Extraordinary Jubilee of Mercy.

[12] According to tradition, Saint Paul's body was buried two miles away from the location of his martyrdom, in the sepulchral area along the Ostiense Way, which was owned by a Christian woman named Lucina.

[13] The circular hole is connected to the tomb by a pipeline, reflecting the Roman custom of pouring perfumes inside the sarcophagus, or to the practice of providing the bones of the dead with libations.

The discovery of the sarcophagus is mentioned in the chronicle of the Benedictine monastery attached to the basilica, in regard to the 19th century rebuilding.

[14] On 6 December 2006, it was announced that Vatican archaeologists had confirmed the presence of a white marble sarcophagus beneath the altar, perhaps containing the remains of the Apostle.

[15][16] A press conference held on 11 December 2006[17] gave more details of the work of excavation, which lasted from 2002 to 22 September 2006, and which had been initiated after pilgrims to the basilica expressed disappointment that the Apostle's tomb could not be visited or touched during the Jubilee year of 2000.

The larger 386 basilica that replaced it had the Via Ostiense (the road to Ostia) to the east and so was extended westward, towards the river Tiber, changing the orientation diametrically.

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