Until the middle of the 19th century it was thought that the present Basilica of San Clemente was that mentioned in 392 AD by St Jerome who wrote that ‘a church in Rome preserves the memory of St Clement to this day.’

In 1857 Fr Joseph Mullooly, O.P., the then Prior of San Clemente, began excavations under the present basilica, uncovering not only the original, fourth-century basilica directly underneath, but also at an even lower level, the remains of a first-century building.

At this third level there are two separate buildings. One is a brick building in the courtyard of which there is a Mithraic temple of the end of the 2nd century. The other is a more magnificent, rectangular structure, constructed around a courtyard.

In the 4th century, the ground-floor rooms of this structure and the courtyard were filled in to the level of the first storey to provide the foundations for a church in memory of Pope Clement. The courtyard of this new level became the nave of the church, while the rooms that once overlooked the old courtyard on either side were converted into the side aisles.

The completed basilica survived until about 1100 AD when it was found that the building was unsafe and should be abandoned. The fourth-century basilica was then filled in with rubble to the top of its pillars and on this foundation a replica of the old basilica was erected.