The Basilica of San Clemente is one of the finest examples of historical and cultural stratification in Rome, with the superimposition of different structures, beginning with the Roman ones of the Republican era, over which a church was built in the 4th century AD. The rectangular Roman building, dating to the early 2nd century AD, is located beneath the church and is surrounded by walls of large tuff blocks. Its structure suggests that the complex was a public building requiring surveillance and was likely used for minting Roman coins. Adjacent to this are the remains of an older Roman house, built in the second half of the 1st century AD: in the basement of the domus, a Mithraeum was installed for the worship of the god Mithras.

The early Christian church was built in 385 and dedicated to Saint Clement, the fourth pope (died 97). It stood until the 11th century, when it was severely damaged during the Sack of Rome in 1084 by a fire started by Norman troops. On the ruins of the church, Pope Paschal II built the upper basilica in 1108.
The load-bearing walls of the lower church are adorned with admirable 12th-century frescoes. One particularly interesting fresco is the so-called Miracle of Sisinnius, one of the miracles attributed to Saint Clement. The image depicts Sisinnius's attempt to interrupt the mass celebrated by Saint Clement, in which his wife Theodora was secretly attending after her conversion, in order to take her away. In the second scene, Sisinnius orders his servants (Gosmario, Albertello, and Carboncello) to bind and drag Saint Clement. Thanks to the saint's miracle, he is miraculously freed from his chains, leaving the servants, blinded like their master, to drag a column in place of his body. In the painting we find one of the oldest testimonies of the Italian vernacular: on the right Sisinnius says to the servants "FILI DE LE PUTE, TRAITE" ("Sons of bitches, pull!"), while in the center are the words spoken by Saint Clement: "DURITAM CORDIS VESTRIS, SAXA TRAERE MERUISTIS", or "Because of the hardness of your hearts you deserved to pull stones".

The interior of the upper basilica is divided into three naves, divided by ancient Roman columns of marble and granite that Carlo Fontana adorned with Ionic capitals. In the naves are three splendid gilded wooden coffered ceilings, adorned with the emblems of Clement XI and containing three paintings depicting the Coronation of Mary, the Glory of Saint Servolo, and the Glory of Saint Clement. The Cosmatesque-style inlaid polychrome marble floor and the marvelous mosaic in the apse, featuring Christ crucified between the Virgin and Saint John the Evangelist, date back to the 12th century. In the current central nave, you can admire the splendid Schola Cantorum (the space reserved for singers), previously present in the lower basilica and moved to the upper level in the Middle Ages. In the Chapel of Saint Catherine, you can admire frescoes depicting stories from the life of the saint, the work of Masolino da Panicale and an expression of early Italian Humanism.

The current façade, sober and elegant, was designed by Carlo Fontana and built in 1716. It is flanked by the bell tower, built between the late 17th and early 18th centuries.