Rome is an exceptional city to walk along and view the monuments of different time periods. One can see Classical, Medieval and Baroque architecture side by side, often within the same block. It is also an outstanding city to walk over buildings of different periods, mostly from Classical Roman times.
Today's Rome is built squarely on top of the bustling and dense metropolis that once ruled the ancient Mediterranean world. What is more, the thick walls of many ancient Roman buildings serve as the foundation of younger buildings, while magnificent coloured marble columns of Classical monuments are also sometimes used in those newer buildings. You can see such columns in the naves of early Christian churches.
The best underground site in Rome is in the Necropolis Vaticana, under the church of Saint Peter. It is a must for any visitor passionate about Roman architecture. Here you can see the fantastically preserved and very well kept Roman Necropolis, dating to Imperial times and built across the Tiber and outside the (then) official city limits. This Vatican area was popular also for sports venues of which little evidence remains, except St. Peter's obelisk. You will have to make a reservation well in advance through the Escavation Office of the Fabbrica di San Pietro.
Cross section and plan of the Necropolis Vaticana located under St. Peter's nave. Image from Wikimedia Commons, scanned by Mogadir, from Pietro Zander: The Necropolis under St. Peter's Basilica in the Vatican, 2009, Rome, Fabbrica di San Pietro.
A new exceptional venue is the excavations of the Domus Romane of Palazzo Valentini, off Piazza Venezia and up the hill to the left of Trajan's column. A reservation is recommended (see the online ticketing info provided by the city of Rome), though you can just walk in and ask for availability because usually you can enter right away. The entrance is located in the courtyard of the building of the Province of Rome. The display - including parts of an ancient Roman house, the baths and a street under the glass floor, with lights and sounds to enhance it - is outstanding. This is top-notch museum technology.
A very important and increasingly popular site is the Church of Saint Clemente with its two underground levels. Under the current ground level of this lovely 12th century church lies a 4th century church, and even further down are the buildings of ancient Rome, built during the heyday of the Colosseum, located nearby. You will find a temple to the god Mithras (a rare sight in the city) and a Roman house made of large stone blocks. Here you can begin to understand how much new sediment and how many new buildings have raised the level of the existing city. No reservation needed.
The Roman temple of Mithras located at the deepest underground level of San Clemente church. Photo by Ice Boy Tell, from Wikimedia Commons.
Two more venues merit attention. One museum that includes underground structures is the Crypta Balbi, part of the National Museum system. A nice surprise is that many buildings in the block are being moved to reveal the Roman theatre complex. Second, if you happen to be strolling in the Celio neighbourhood, you can visit the Case Romane del Celio, a Roman early 5th century apartment building with well-preserved rooms.
In addition to the Ancient Forum, sites below the current ground level which show the richness of the Classical buildings are not always evident as you walk in the open air of the city, but Largo Argentina is an exception. It is an exposed site, opened early last century. Please note that this list of underground venues does not even consider the catacombs...