5 minutes away form the Colosseum is the best place in Rome to see the layer-cake effect of its history in action: church piled atop church piled atop pagan temple. This situation is far from unique in Rome, almost the entire city is built directly on top of the ancient one, but what's special about San Clemente is that we can actually clamber down into those underground levels.
San Clemente's upper church—The 12th to 15th centuries
The upper church, built in 1108 and run by the convent of Irish Dominican monks who rediscovered the lower levels in the 19th century—is beautiful enough to stand out on its own.
San Clemente's lower church—The 4th century
It preserves a few crude frescoes from the Paleo-Christian era, including the Life of St. Clement on the wall before you enter the nave and the Story of St. Alexis on the left wall of the nave itself
San Clemente's Mithraic temple and Roman palazzo—The 1st to 2nd centuries
The altars of both later churches are placed directly above a Mithraeum with an altar of a pagan Temple to Mithras from the AD late 2nd century. As part of their rituals, Mithraic priests would also sacrifice bulls until the blood flowed into troughs, which followers would then scoop out with their arms to bathe in. Sounds nasty, but back in the day it was a hugely popular cult—certainly it had far more acolytes in the first few centuries AD than another of the many nascent cults swirling around Imperial Rome: Christianity.
Next to this temple are the buried remains of an intact Roman palazzo of the AD 1st century. You will hear the sound of rushing water from the ancient pipes and aqueducts between the walls. In one room you can even take a drink from the sweet spring water gushing out of an ancient pipeline to be routed along a small aqueduct set into the wall.
The Case Romane (Roman Houses) are located between the Colosseum and the Circus Maximus. The houses were opened to the public in 2002.
Together with the excavation of San Clemente they represent one of the most fascinating subterranean spaces in Rome due to their extremely well conserved frescoed rooms and because of the artistic and religious value of the site.
The houses, known also as the home of the martyrs John and Paul, contain more than four centuries of history and attest to the coexistence and transition between paganism and Christianity.
The frescoed rooms, originally shops and storerooms of a multi-storied working class building, were in fact transformed during the 3rd century AD into an elegant upper class residence. Within the rooms, you can admire some of the most beautiful frescoes of Late Antiquity.