Basilica of San Clemente, Rome

Five minutes from the Colosseum, behind a plain Baroque front, is the best single lesson in Rome. A twelfth-century basilica stands on a fourth-century basilica, which stands on a Roman street of the first century with a temple of Mithras in it. You go down the stairs and you go back a thousand years, and at the bottom you can hear an underground river that kept archaeologists out of the temple for nearly fifty years.

Three churches, one hole in the ground

Start at the bottom. In the first century AD this was a city block: a courtyard house, and beside it, across a narrow alley, a large public building of the warehouse type, its bricks stamped AD 90–96. Both went up over ground cleared by the Great Fire of AD 64. Around AD 200 a Mithraeum was installed in a room of the block. By the end of the fourth century the Mithraeum was abandoned and the whole level was filled in and built over.

On top of it, in the fourth century, a Christian basilica was formed by roofing and adapting the Roman building above. St Jerome mentions a church here in 392, which makes the titulus Clementis one of the oldest title-churches in Rome. It was decorated continuously from the sixth to the eleventh century and is reckoned to hold, after Santa Maria Antiqua, the largest body of early medieval wall painting in the city.

Then the Norman sack of 1084 wrecked the district. Rather than repair the old church, they filled it with rubble and built a new one on top of it, re-using the old walls as foundations. That new basilica — the one you walk into — went up under Cardinal Anastasius, around 1099–1120, in the pontificate of Paschal II, who was himself elected in a conclave held on this site.

Father Mullooly digs a hole

The lower church was forgotten for seven hundred years. In 1857 the prior of the convent, an Irish Dominican named Joseph Mullooly, started digging under the high altar, and kept going until about 1870, uncovering the fourth-century basilica and reaching the Roman level below it. In 1863 he identified the tomb of St Cyril. In 1867 his men found the Mithraeum — and could do nothing with it, because it was under water.

The water beat them for forty-seven years. It was another Dominican, Fr Louis Nolan, who in 1912–14 traced the spring feeding it, tapped it, and drove a drainage tunnel from San Clemente towards the Colosseum. The convent still takes its water from it, and you can hear it running as you walk. The Irish Dominicans have held the basilica since 1677, when they were given it as a refuge, and they run it, dig it and guard it still.

The visitor's cheat sheet

Level one: the upper basilica

The atrium

A colonnaded courtyard with a fountain in the middle, columns robbed from grand Roman buildings, and a working convent around it. The medieval narthex was replaced by the present sober front in 1719, by Carlo Stefano Fontana, during Clement XI’s restoration.

The apse mosaic

The reason art historians come. The whole conch is gold, and out of a clump of acanthus at the foot of the cross grow enormous vine scrolls that fill every inch of it. In the middle, Christ crucified between the Virgin and St John, with twelve white doves perched along the cross for the twelve Apostles and the hand of God reaching down from above with a wreath. From the foot of the tree run the four rivers of Paradise, and two deer drink at them — Psalm 42, as the deer longs for flowing streams.

Look inside the scrolls. There are doctors of the Church in there, but there are also peasants: a shepherd, a woman feeding hens, a man with a bird. The vine is the Church and everybody is inside it, doing their jobs. Below, twelve sheep process towards the Lamb; above the arch, Bethlehem and Jerusalem, prophets and saints. An inscription runs beneath it comparing the Church to a vine that the Law withered and the Cross made bloom.

The floor and the choir

The nave floor is Cosmatesque: swirling geometric bands of cut marble, most of it salvaged imperial stone — yellow giallo antico from Tunisia, green porphyry from Sparta, imperial red porphyry from Egypt. Nobody was quarrying that in the twelfth century; they were sawing up whatever the ancient city had left lying about.

In the middle of the nave is the schola cantorum, an enclosure of upright marble panels carved with fish, anchors, doves and vine leaves. Here is the thing to know about it: it is sixth-century, and it was carried up out of the church below when the new basilica was built. Several panels carry the monogram of Pope John II (533–535), who gave them — he was born Mercurius, and changed his name on election because a pope could not be named after a pagan god, the first pope to do it. That monogram is how the panels were dated, and it is the single clearest object in the building for understanding what San Clemente is: a church that recycles itself.

The Chapel of St Catherine

Immediately on your left as you come in from the side door, and constantly walked past. It was paid for by Cardinal Branda Castiglione, a Milanese humanist, and frescoed by Masolino da Panicale in the later 1420s — the first chapel frescoed in Rome after Martin V’s election brought the papacy back to the city.

Left wall: the life and death of St Catherine of Alexandria — the disputation with the philosophers, the wheel, the beheading. Right wall: the life of St Ambrose, patron of Milan, which is the patron making a political point. Altar wall: the Crucifixion; over the entrance, an Annunciation. The architecture inside the scenes is built in the newly invented one-point perspective, and you can watch a painter enjoying a new toy.

Whether Masaccio had a hand in it — the two collaborated elsewhere, and he died in 1428 — has been argued for a century, usually over the Crucifixion or the Annunciation. Most scholars now give the execution to Masolino. It is an open question, not a fact, whichever way your guide states it.

Level two: the 4th-century basilica

Down the stairs from the sacristy. It is cool, dim and brick-vaulted, with the foundation walls of the church above driven straight through it, and the walls carry frescoes from the sixth to the eleventh century.

Four of the great late-eleventh-century paintings were paid for by Beno de Rapiza and his wife Maria Macellaria — Maria the butcher’s wife. They are lay donors, not aristocrats, and they put themselves and their children into the pictures.

Look for the legend of St Alexius, the nobleman who fled his own wedding, came home unrecognised and lived seventeen years under the staircase of his father’s house; and the miracle at the Black Sea, in which the sea draws back once a year to reveal Clement’s shrine, a child is left behind when the tide returns, and the mother comes back twelve months later to find him alive. St Clement himself was martyred by being tied to an anchor and thrown into the sea, which is why an anchor is carved on the ciborium upstairs.

The Sisinnius fresco

This is the most quoted wall in Rome, and it is small, high and badly lit, so know what you are looking for. The prefect Sisinnius, suspecting his wife Theodora of following Clement, follows her to a service and is struck blind and deaf. He orders his servants to seize the saint. They lay hold instead of a stone column and heave away at it while Clement stands beside them, untouched.

The words are painted beside the speakers’ mouths, like speech balloons. Sisinnius, in eleventh-century Roman street language, is bawling at his men: “Fili de le pute, traite! Gosmari, Albertel, traite! Falite dereto colo palo, Carvoncelle!” — roughly, “Sons of bitches, pull! Gosmarius, Albertellus, pull! Carvoncellus, get the pole in behind it!” Clement answers, in Latin: “Duritiam cordis vestris, saxa traere meruistis” — “For the hardness of your hearts, you have deserved to drag stones.”

It is generally cited as the earliest written Italian used to tell a story, and it contains an obscenity, which is why every guide in Rome enjoys it. But notice what the painter is doing: the saint speaks Latin and the thugs speak the gutter. The language is carrying the argument. And the joke is good in any century — they are swearing themselves hoarse at a lump of masonry while the man they came for watches.

St Cyril

Also down here is the site of the grave of St Cyril, who with his brother Methodius invented the Glagolitic alphabet and evangelised the Slavs. The brothers recovered at Chersonesus in the Crimea what they believed were the relics of St Clement and brought them to Rome in 867; Cyril died in the city in 869 and was buried in the basilica of the saint whose bones he had carried home. His shrine was moved up to the new church when the old one was buried, and the walls around it upstairs are crowded with plaques and mosaics given by Czech, Slovak, Croatian, Bulgarian and Macedonian churches. John Paul II named Cyril and Methodius co-patrons of Europe in 1980.

Level three: the Roman street and the Mithraeum

Another staircase, and you are on first-century ground, something like eighteen metres below the modern street. You can walk the alley between the two Roman buildings. The walls are brick-faced concrete and the vaults are the real thing, unrestored.

The Mithraeum is a rectangular chamber with a stone bench running down each side, where initiates reclined for the ritual meal, and a barrel vault pierced with niches for lamps and carved to represent the cave — and the cosmos. In the centre stands the altar, a block of Parian marble a little over a metre high, carved on all four faces. On the front, Mithras in his Phrygian cap kills the bull, while a dog and a snake go for the wound and a scorpion for the genitals, a raven watches from the rock, and Sol and Luna look on from the corners. On the sides are the torchbearers, Cautes with his torch up and Cautopates with his down.

Next door is a vaulted room read as the mithraic school, where initiates were taught. Stop in the corridor and listen: the rushing water is the spring Fr Nolan tapped, running to the Cloaca Maxima system and out toward the Colosseum. It is the most memorable thing in the building and it costs nothing to notice.

Tickets and tours

Don't miss

• The apse mosaic A gold conch filled with one enormous vine, twelve doves on the cross, four rivers and two deer. The best 12th-century mosaic in Rome and free to look at.
• The monogram of Pope John II On the choir panels in the nave: 6th-century furniture, hauled up from the church below, signed by the pope who gave it.
• Masolino's Chapel of St Catherine Just inside the side door, and walked past by nearly everyone. The first chapel painted in Rome after the papacy came back.
• The Sisinnius fresco Speech balloons, an obscenity, and the earliest written Italian used to tell a story — with the saint answering in Latin.
• The Mithraeum Bench, cave-vault and tauroctony altar, 18 metres under a Christian basilica.
• The sound of the water The spring that kept archaeologists out of the Mithraeum for 47 years, still running past your feet.

Insider tips

Take a layer, even in August. It is ten degrees cooler down there and very humid; glasses and lenses fog on the way down and the floors are damp and uneven.

Do the upper church first, then the excavations. The stairs are a one-way door in practice: the concentration goes underground and does not come back.

Read the Sisinnius text before you go down. It is high, small and unlit, there is no translation on the wall, and it is the thing you will remember.

Pair it with San Giovanni in Laterano rather than the Colosseum. Ten minutes east, the mother church of Rome, and the reason this basilica is called al Laterano.

Where to stay and eat nearby

You are in the middle of the tourist crush between the Colosseum and the Lateran, so the restaurants immediately around the church charge accordingly. Walk five minutes into Monti, north-west, or towards San Giovanni, and both the food and the prices improve sharply. For staying, Monti is the pleasant choice within walking distance of everything; the streets right by the Colosseum are convenient and noisy.

More churches in Rome

• St John Lateran — ten minutes east, the cathedral of Rome and the other half of this church's name.
• Santa Maria Maggiore — for the other great mosaic cycle, and a nave that has not changed since the fifth century.
• The Pantheon — the other Roman building that was saved by being turned into a church.

See all the churches worth visiting in Rome →