The archaeological traces of the basilica's history were discovered in the 1860s by Joseph Mullooly,[1] Prior of the house of Irish Dominicans at San Clemente (1847–1880).

[2] The lowest levels of the present basilica contain remnants of the foundation of a possibly republican era building that might have been destroyed in the Great Fire of 64.

The main cult room (the speleum, "cave"),[4] which is about 9.6m long and 6m wide, was discovered in 1867 but could not be investigated until 1914 due to lack of drainage.

[9] One of the rooms adjoining the main chamber has two oblong brickwork enclosures,[10] one of which was used as a ritual refuse pit for remnants of the cult meal.

The last major event that took place in the lower basilica was the election in 1099 of Cardinal Rainerius of St Clemente as Pope Paschal II.

Apart from those in Santa Maria Antiqua, the largest collection of Early Medieval wall paintings in Rome is to be found in the lower basilica of San Clemente.

Below this last scene is one of the earliest examples of the passage from Latin to vernacular Italian: a fresco of the pagan Sisinnius and his servants, who think they have captured St. Clement but are dragging a column instead.

The saint speaks in Latin, in a cross-shaped inscription: Duritiam cordis vestris, saxa trahere meruistis, which means "You deserved to drag stones due to the hardness of your hearts."

A now-outdated hypothesis held that the original church had burned out during the Norman sack of the city under Robert Guiscard in 1084, but no evidence of fire damage in the lower basilica has been found to date.

The basilica church behind it is in three naves divided by arcades on ancient marble or granite columns, with Cosmatesque inlaid paving.

[16] The carved and gilded coffered ceilings of nave and aisles, fitted with paintings, date from this time, as do the stucco decor, Ionic capitals and frescos.

During the Second World War, Jewish religious services were conducted in the Basilica di San Clemente, since it was under Irish diplomatic protection, under a painting of Tobias.