Well, if so, you've only scratched the surface.
Underground, beneath the Coliseum lies a rabbit-warren of rooms where the death defying spectacles were prepared. Beneath that, archaeologists have excavated the skulls of tigers, giraffes, bears, and other animals used in the shows.
And those churches you've visited for their renaissance art most likely harbor pagan secrets below their floors as well.
Basilica of San Clemente
One of the most fascinating adventures I've taken recently was to descend into the underground below the 12th century Basilica of San Clemente. Here there are two excavated levels, one revealing the plan of a 4th century Basilica, and the other some 1st century Roman buildings. In one of these is a perfect example of a temple of Mithras, a Persian God who probably migrated back to Italy with soldiers and slaves. (More on Mithras)
(In summer, the Basilica offers classical music concerts in the enclosed outdoor courtyard. The Rome New Opera Festival is to be held there. If you'd like to spend an enchanting evening, find the dates of the concert posted outside the Basilica. You can purchase tickets at many of the small tabacchi (cigarette stores) across the street.)
Vital Info: Basilica of San Clemente
Location : Via di San Giovanni in Laterano, (Piazza S. Clemente)
Open daily 9:00-12:00 and 15:30-18.30
Cost : 5 Euros (check website for current prices)
Case Romane del Celio
Below the Basilica of Ss. Giovanni e Paolo are a complex of Roman houses restored by the Soprintendenza Archeologica di Roma and the Soprintendenza per i Beni Artistici e Storici.
Location: Cilvus Scauri (Map and information on Mark's Travel Notes: Rome - Case Romane del Celio.
Open every day except Tuesday and Wednesday between 10am and 1pm and from 3pm to 6pm.
Cost: 6 Euros ( check website for current prices)
Nero's Domus Aurea
Domus Aurea is Closed at this time. Another popular underground tourist destination is Nero's Domus Aurea. While many sites still encourage reservations in advance, I've found that you can usually walk up and purchase a ticket for the next available tour.
Vital Info: Nero's Domus Aurea
Hours 9:40-6:40pm (except Saturday, when it's only open until 11. Closed Tuesday.
Prices : 6.50 Euros, plus 1.50 Euro booking fee and 4 Euro prebuy fee.
Getting There : The Domus is on the Viale della Domus Aurea across from the Coliseum. The easiest way is to take the Metro LINE "B" getting off at the Station Colosseo.
Visitors point to the many layers of the Crypta Balbi as a way to put into perspective the forces that buried classic Rome. Inside is a section of Museo Nazionale Romano where you'll learn about the occupation layers you'll see.
Vital Info - Crypta Balbi
Hours 9am - 7:45 pm, closed Mondays
Prices : 4 Euros
Address : Via delle Botteghe Oscure, 31
Necropolis - St Peter's Basilica
Here's an acclaimed site that needs some planning in advance to visit. Besides two-story high mausoleums, there's an entire city under the Vatican.
St. Peter's tomb is reported to be here, but the excavation seems to have been bungled, in part due to the suspiciously watchful eye of the Vatican. You can read the whole story in the entertaining and informative "When in Rome : A Journal of Life in Vatican City" by Robert J. Hutchinson (compare prices).
For detailed info on applying for a tour of the Vatican excavations see: Vatican Excavations - Tips for Visiting the Vatican Scavi.
There's more...Underground Rome, or Roma Sotteranea
There are other subterranean visits to be made in Rome, and an enormous compendium of information on just about everything underground in Rome is to be found at Roma Sotteranea (English) which also organizes tours.
Roma Sotteranea has recently updated their website and expanded their tour offerings. You can now visit many sites, above and below ground, normally closed to the public through the organization, whose main activity is to document and explore underground archaeological sites in collaboration with the Superintendent of Archaeology. Even if you don't go on a tour, you can find out a wealth of information on this site about many of the "invisible cities" lurking underground in Rome. They also offer a newsletter of their activities.
Underground Tours and Excursions Near Rome
Many towns in Lazio and nearby Umbria sit atop ancient and recent excavations in the relatively soft tufa rock. Folks have been creating everything from bomb shelters to wine cellars, underground churches to pigeon-breeding rooms in these excavations--some of which threaten to collapse the cities that are built over them.
Mary Jane Cryan describes many of them in Mysterious Underground Sites near Rome. We recommend the Orvieto underground tour (you can also visit the Etruscan Tombs a bit down the hill from Orvieto as well).