The present San Clemente was built around 1100. Below it is a 4th century church, and below that a Roman house in which it is believed Christians worshipped until the 4th century church was built.
The oldest level is thought to be the titulus Clementis, one of the first parish churches in Rome, and probably belonged to the family of Titus Flavius Clemens
, consul and martyr and a contemporary of Pope St Clement. Set right next to a pagan temple, a Mithraeum or Temple of Mithras, it was one of the first churches in Rome.
A proper church was built after the Edict of Milan
was passed in 313, allowing Christians to practise their religion openly. The first written evidence of this church comes from the pontificate of Pope Siricius
(384-399), when a church dedicated to St Clement is mentioned. The older buildings were filled in, and a church occupying about half that are was built. The Mithraeum continued to exist until 395, when all pagan cults were outlawed. The property was taken over by the clergy of S Clemente, who filled it in and built an apse to the church.
Pope John II
(533-535) was a great benefactor of the church - he had been cardinal priest of S Clemente from c. 532 until his election as pope in 533. His name can be seen inscribed on several slabs in the church.
The church was severely damaged by the Normans under Robert Guiscard
in 1084. It became unsafe, and the titular priest of the church, Cardinal Anastasius (cardinal c. 1099 - c. 1125) filled it in and had a new church built.
Pope Clement XI
(1702-1715) had the church restored, with Carlo Stefano Fontana as the architect.
The first excavation of the lower church was carried out by Fr. Joseph Mulooly O.P. 1857-1870, with the cooperation of Giovanni Battista de Rossi
. Fr. Louis Nolan O.P. carried out further excavations 1912-1914, and since then more or less continuous work has been going on.