As early as 200 the burial place of the great Apostle in the Via Ostia was marked by a cella memoriæ, near which the Catacomb of Comodilla was established. Constantine, according to the "Liber Pontificalis", transformed it into basilica.
In 386 Theodosius began the erection of a much larger and more beautiful basilica, but the work including the mosaics was not completed till the pontificate of St. Leo the Great. The Christian poet, Proudentius, describes the splendours of the monument in a few, expressive lines. As it was dedicated also to Saints Taurinus and Herculanus, martyrs of Ostia in the 5th century, it was called the basilica trium Dominorum.
Of the ancient basilica there remain only the interior portion of the apse with the triumphal arch and the mosaics of the latter; the mosaics of the apse and the tabernacle of the confession of Arnolfo del Cambio belong to the 13th century. In the old basilica each pope had his portrait in a frieze extending above the columns separating the four aisles and naves.
In 1823 a fire, started through the negligence of a workman who was repairing the lead of the roof, resulted in the destruction of the basilica. Alone of all the churches of Rome, it had preserved its primitive character for one thousand four hundred and thirty-five years. The whole world contributed to its restoration. The Viceroy of Egypt sent pillars of alabaster, the Emperor of Russia the precious malachite and lapis lazuli of the tabernacle. The work on the principal facade, looking toward the Tiber, was completed by the Italian Government, which declared the church a national monument. The interior of the walls of the nave are adorned with scenes from the life of St. Paul in two series of mosaics.
The graceful cloister of the monastery was erected between 1220 and 1241. The sacristy contains a fine statue of Pope Boniface IX. In the time of Gregory the Great there were two monasteries near the basilica: St. Aristus's for men and St. Stefano's for women. Services were carried out by a special body of clerics instituted by Pope Simplicius. In the course of time the monasteries and the clergy of the basilica declined; St. Gregory II restored the former and entrusted the monks with the care of the basilica. The popes continued their generosity toward the monastery; the basilica was again injured during the Saracen invasions in the 9th century. In consequence of this Pope John VIII fortified the basilica, the monastery, and the dwellings of the peasantry, forming the town of Joannispolis, which was still remembered in the 13th century.
In 937, when St. Odo of Cluny came to Rome, Alberico II, patrician of Rome, entrusted the monastery and basilica to his congregation and Odo placed Balduino of Monte Cassino in charge. Pope Gregory VII was abbot of the monastery and in his time Pantaleone of Amalfi presented the bronze gates of the basilica, which were executed by Constantinopolitan artists. Pope Martin V entrusted it to the monks of the Congregation of Monte Cassino. It was then made an abbey nullius. The jurisdiction of the abbot extended over the districts of Civitella San Paolo, Leprignano, and Nazzano, all of which formed parishes; the parish of San Paolo in Rome, however, is under the jurisdiction of the cardinal vicar.