Here's where most-first time visitors to Rome get it wrong: they head straight for St Peter's Cathedral. St Peter's is a magnificent building, containing superb works of art; however its size – not to mention the size of the crowds – can be so overwhelming, visitors don't set foot in another church for the rest of their visit.
And that's a shame, because for 1600 years, building churches is what Rome did. If you wanted your church to get noticed, you had to make it pretty extraordinary, which is why today, there are churches built into and over Roman ruins, decorated with human bones, and hung with museum-quality art.
Here are our 10 favourite churches in Rome. Some are well known; most are off the tourist trail; but you won't have to queue at a single one.
For ancient ruins
Visit Basilica di San Clemente
Rome is like millefeuille pastry, where the past is piled layer upon layer. Stick a shovel in the ground and you are literally digging up history. The 12th-century Basilica di San Clemente, for instance, sits above a 4th-century church, built in turn above a 2nd-century pagan temple and a 1st-century Roman house. What makes San Clemente special is that here you can explore one layer after another. Take a walk around the street-level basilica first: particularly lovely is the striking mosaic showing Christ on a crucifix that turns into a living tree. Take the stairs on the right side down to the fourth century church, damaged beyond repair during a Norman attack in the 11th century. The frescoes you see depict scenes from the life of Saint Clement, and are 1000 years old. From here, another set of stairs takes you down to the shrine of the Persian god Mithras, whose altar depicts the god slaying a bull. The sound of running water comes from drains dating back to the Roman republic.
For glittering mosaics
Basilica di Santa Prassede
The small but sumptuous Basilica di Santa Prassede, one of Rome's oldest surviving churches, is remarkable for its dazzling Byzantine mosaics, and for the medieval power plays that lie behind them.
Santa Prassede was part of a 9th-century building boom launched by Pope Paschal, in a campaign to replace the city's decrepit churches, many of which were by then 400 years old. As it happened, Pope Paschal had recently fallen out with the Byzantine Emperor in Constantinople, so when the Emperor issued an edict outlawing the icons which had until then been a signature feature of Byzantine churches, the pope not only refused to obey the edict; he also decided to add as many icons and mosaics to his new churches as he could.
Constantinople's unemployed icon makers, who were no fools, headed straight to Rome, where the Pope put them to work creating masterpieces such as Santa Prassede's Chapel of Zeno, where every surface is covered with mosaics. The church has other magnificent mosaics as well. The one above the main altar is particularly striking, not least because the white clad holy men look endearingly like cheerleaders heading on to the football field at half-time.
For an artistic revolution
San Luigi dei Francesi
Political revolutions often have a ground zero – the site of the first protest, or riot, or massacre. Artistic revolutions, not so much. But the pretty church of San Luigi dei Francesi, near Piazza Navona, launched an artistic revolution 400 years ago when it unveiled three paintings by Caravaggio.
No one painted like Caravaggio did: the action dramatically framed by shadows, the people recognisable as working men and women, right down to their dirty soles. He achieved some critical acclaim with his earliest works, but no one thought he would ever crack the lucrative church market, where artistic careers were made.
Now the church of San Luigi dei Francesi had a problem. The painter commissioned to create three paintings for the Contarelli chapel had missed his deadline – by 15 years. The congregation petitioned the pope, declaring it a national disgrace that the chapel was still boarded up. In desperation, they finally turned to a painter who was willing, able and available - Caravaggio. His paintings, depicting scenes from the life of Saint Matthew, were an instant, if controversial, success. They made Caravaggio's career, and changed the artistic landscape.
For the gory details
Santo Stefano in Rotondo
Thanks to its off-the-beaten track location, around 10 minutes from the Colosseum, Santo Stefano is one of Rome's better-kept secrets. The first thing you notice is its shape: it is one of the few remaining round churches in Rome. What really sets this church apart, however, is the frescoes on the walls, vividly depicting 34 different saints being martyred.
It's not a sight for the squeamish: according to Charles Dickens, "...such a panorama of horror and butchery no man could imagine in his sleep, though he were to eat a whole pig raw, for supper." The images could illustrate a primer on how to kill Christians: you can cut their breasts off, roast them on a grill, pour molten lead down their throats… None of the saints look disturbed by their torment; one presumes the rapturous looks on their faces depict their delight at heading to heaven. The effect is particularly odd in one fresco where a number of martyrs are being boiled alive – at first glance, they seem to be enjoying a dip in a hot tub.
Visit Basilica di Santa Maria degli Angeli de dei Martiri
When you have as much history lying around as the Romans do, you have to find new ways to deal with it. At San Clemente, they built over it. At Santa Maria degli Angeli, by contrast, they built inside it.
This is the only church in Rome built inside ancient baths, specifically the Great Hall of the Baths of Diocletian. Michelangelo was the architect in charge, and he was clearly at pains to preserve the ancient Roman feel. He didn't even create a facade for the church: this must be the only church in Rome that has crumbling exposed brick on one side of the entrance. He did raise the floor to the 16th-century street level, but even so, the dramatic proportions of the original are still evident: the transept is 90 metres long and still almost 30 metres high.
Take a peek into the side rooms: in one of them, you will find information about the building's history, and be able to peer out into what remains of the rest of the crumbling complex.
For underground treasures
Basilica di Santa Cecilia in Trastevere
Saint Cecilia was just 14 when she was martyred. After locking her in her own steam room for three days in an attempt to suffocate her, the executioner tried three times to cut off her head. She lingered for another three days, reputedly converting several people to Christianity before she died.
The story may be grisly, but Cecilia's church - erected on the site of her home - has several delightful features, not least the heartbreakingly lovely statue of her corpse, sculpted by an eyewitness.
Down in the basement, you can walk through the ruins of an ancient Roman house and look out to the old Roman street that runs past. The most spectacular feature, however, is the underground sacristy, a vision of medieval splendour glowing in gold and blue, with angels looking down from above. Something most visitors don't realise: it's not medieval at all. This version of the sacristy was created in the 19th century, by a restorer who was horrified at the wholesale destruction of Rome's medieval buildings. This lush interior was designed to remind Romans of what was being lost.
San Carlo alle Quattro Fontane
It was a clash of the titans. Two great architects dominated Rome in the 17th century: Gian Lorenzo Bernini and Francesco Borromini. Although Borromini originally worked for Bernini, they had a grand falling out, and spent the rest of their lives locked in fierce rivalry. For many years Bernini, under the patronage of Pope Urban VIII, was the star performer. After Urban's death, his successor, Innocent X, ditched Bernini and instead supported Borromini.
Innocent may have decided to embrace Borromini after seeing his beautiful church of San Carlo alle Quattro Fontane. It is a stark contrast to the dramatic baroque interiors that were Bernini's signature. Borromini was an architect who enjoyed working in a minor key. Against stark white interiors, this church mixes concave and convex forms to create a sense of movement. The dome seems to float above the walls. It is exquisitely simple, a church almost Zen in its philosophy, and provides a beautiful contrast to the richly decorated cloister.
For Gothic grandeur
Santa Maria Sopra Minerva
As the name suggests, a Roman temple to Minerva once stood on this spot. What sits here today is a relic of a different sort: one of the few remaining Gothic churches in Rome. Gothic churches are common throughout France, but the Gothic movement passed Rome by, not least because during its heyday, the popes were based in Avignon. So you won't find anything else in Rome quite like Santa Maria Sopra Minerva, with its vaulted arches and its blue and gold colour scheme.
There is plenty to see, including no fewer than three papal tombs – the Medici popes Leo X and Clement VII, and Paul IV – as well as the body of Saint Catherine of Siena (her head is in Siena). Art lovers will also want to inspect the lovely frescoes by Filippino Lippi, and the church's secret treasure: a little-known Michelangelo statue, Cristo Risorto.
For spine-tingling shivers
Santa Maria della Concezione dei Cappucini
It's not so much the church itself that is the attraction here; what really draws visitors is the cemetery that lies beneath it. The Capuchin monks filled the six-room crypt with their clever craftwork, using a somewhat unusual choice of materials. Here, everything is made of the bones of deceased monks, from light fixtures made of femurs to an arch containing hundreds of skulls.
Around 4000 monks, buried between 1500 and 1870, are believed to have contributed their bones to this rather macabre artwork. The monks – buried without coffins, in soil brought all the way from Jerusalem - shared their graves on a rotating basis, with the oldest corpses being removed to make room for new arrivals. A body typically spent 30 years decomposing before being dug up and added to the artwork. Perhaps unsurprisingly, the Marquis de Sade was impressed by the place, writing, "I have never seen anything more striking."
For majestic masterpieces
Santa Maria del Popolo
You can stand on the Piazza del Popolo for quite a long while without seeing anyone set foot inside this church, tucked away on one side of the busy plaza. Those who do venture inside, however, will be rewarded with the chance to check out one of the best art collections of any church in Rome.
It is hard to know where to start. The first chapel on the right contains some beautiful Pinturicchio frescoes. Then there is the Chigi Chapel, originally designed by Raphael, who worked on the vault mosaic and the statues of Jonah and Elijah. That wasn't quite enough for the Chigi family: a century later, they commissioned the mighty Bernini to add some more statues and decoration.
By the altar, the Cerasi Chapel contains two of Caravaggio's masterpieces, the Crucifixion of St Peter and Conversion of St Paul. Predictably, these also caused a storm of controversy, particularly the former: critics were shocked at the foreground of the painting, where one of the men hauling on the cross sticks his bum in the viewer's face.
The elegant rooms at Babuino 181 are scattered through different palazzi near the Spanish Steps, but there is a helpful concierge and a gorgeous bar. Rates start at 230 euros. See mrandmrssmith.com
High-speed trains connect Rome with other cities in Italy and beyond. Rail Europe offers a wide range of rail passes and tickets. Visit raileurope.com.au for more information and ongoing deals.
Gusto, Via della Frezza 16, gusto.it; Il Tempio di Iside, Via Verri 11, isideristorante.it; Glass, Vicolo Dè Cinque 58, glass-restaurant.it/en.
The writer travelled courtesy of Rail Europe and Mr and Mrs Smith.