The Duke of Wellington saw Napoleon naked every day. The perfect muscular chest of his former enemy must have become, over time, as familiar to him as his own ageing flesh. Antonio Canova's nude colossus of Napoleon Bonaparte stands to this day in the spiralling stairwell of No 1 London, the house at Hyde Park Corner that belonged to the general who defeated Napoleon at Waterloo. In Apsley House you can still see the Duke's art collection - the equestrian portrait by Goya and early paintings by Velázquez. And you can see the godlike Napoleon, presented to Wellington by a grateful nation as a joke on the defeated French emperor.

Napoleon himself commissioned Canova's statue. He was proud to secure the services of the Venetian sculptor who was renowned across Europe as an exponent of neoclassicism, the style that aspired to recreate not just the appearance of ancient Greek art but its ethos - "the Greek ideal". In Rome in the 18th century, the German scholar Johann Joachim Winckelmann had shown that most of the statuary to be seen in the great collections - of the Farnese family, the Duke of Tuscany or even in the Vatican - was mere Roman hackwork, a copy of Greek art whose originals were purer and nobler. He identified what he claimed was the true character of the best, or "classical", ancient Greek art. At its moral heart stood the nude male body: the body of Apollo, of the athlete, the soldier, the citizen.

Napoleon might have done well to read what Joshua Reynolds, theorist as well as painter, had to say on the subject in his Discourses: Greek statesmen were idealistic enough to have themselves portrayed naked, he wrote, but moderns lacked that innocence. Even in France, where the paintings of David had given a classical authority to revolution, a naked statue of Napoleon was going too far.

Today, probably nothing so alienates us from the high art of the European past as its most prestigious subject - the male nude. Visit any old European museum, from Naples to Bloomsbury, and they have more marble statues of disrobed gods and heroes than they can reasonably display. Once these nudes were considered the apex of European culture. Today we don't really know what to do with them, and the reason for this was anticipated when parliament presented Canova's Napoleon to the Duke of Wellington as a ludicrous example of imperial art. Let's face it: the male nude is embarrassing.

Centuries of European artists and art lovers depicted and looked at naked men in what was supposedly a disinterested and entirely cerebral way, as the embodiment of an athletic, spiritual and even political ideal. This purportedly had nothing to do with sex. But it is impossible for us to accept that nude images can be asexual, so it is impossible for us to take seriously this lost aesthetic.

And yet we're more neoclassical than we think we are. To see this, you have only to open a fashion magazine. In fashion in the past few years, the male nude has been re-exposed. Think Calvin Klein underwear or Gucci and, most of all, consider a current advertising campaign for Dolce & Gabbana, in which young men stand around in a straw-spattered photographer's studio while an older man - the artist figure - directs the scene: in each image, nudity is at the tense heart of a visual drama involving a body splayed naked on the ground, or posed with legs cocked as if astride someone.

These photographs quote Caravaggio, of course. Caravaggio is the one master of the male body with whom our culture feels happy, because we know he's in on the joke. He is clearly not an artist of the "ideal", not a noble and disinterested celebrant of the muscular stomach. In his painting of Bacchus, in the Uffizi Gallery in Florence, the god of wine is a Roman street urchin with black eyes and black - apparently made-up - eyebrows, looking back at you as you contemplate a chest pale as marble: a statue come to dangerous life. Bacchus proffers a glass of blood-red wine and, as its surface ripples, Caravaggio acknowledges the sensuality disavowed by the collections of nudes in Roman cardinals' palaces.

The Dolce & Gabbana ads cite Caravaggio, a painter whose memory was almost entirely suppressed in the 18th and 19th centuries when the "Greek ideal" of the male nude was at its loftiest. Yet look closer and these images offer a key - or rather Caravaggio offers a key - to the classical tradition of the nude. Take the curious pose of the model with his legs apart, as if straddling someone. It echoes Caravaggio's Victorious Cupid, his most unambiguous image of the god of love as a street kid wearing black wings, crushing learning, art and culture beneath his foot. Yet his painting is itself a quotation: the boy stretches and strains to achieve the pose of the young man bestriding an older man in Michelangelo's sculpture Victory. With Victorious Cupid, Caravaggio slyly mocks the biography written by Michelangelo's pupil Condivi in the 16th century, which claims that the great man's lifelong love of the male body was purely Platonic. But it is homage, too.

We like to think of the past as an icy monolith - as cold as Canova - from which we romantically escape. In reality, it is as full of tensions as a torso sculpted by Michelangelo. And the fact is, sex never was very far from the art of the male nude.

In the entrance hall of the British Museum, a vast, monumental staircase ascends to a landing whose empty expanse sets off a single masterpiece of classical sculpture: the Discus Thrower. Chest at an angle, sides creased in the moment before hurling his flat disc, this Olympic athlete is the poised epitome of the Greek ideal. And yet, like the vast majority of the works by which we know classical Greek art, this is a Roman copy. It belonged to the emperor Hadrian and comes from his villa at Tivoli, near Rome.

Only in the rare originals that survive of Greek art - paintings on vases, a handful of bronze statues, the Elgin marbles - can we know Greek images of nudity directly. Mostly, we encounter this art through Roman collectors for whom it was already experienced at one remove. Romans displayed Greek nudes, but thought of them as exotic; they themselves would usually pose in armour.

The most passionate Roman collector of Greek art was Hadrian, who enjoyed not just Greek art but Greek love. His fascination with Greek culture was inseparable from his cult of his male lover, Antinous.

It would be so easy to "deconstruct" the tradition of the male nude by telling stories like this: in the British Museum, the Discus Thrower arcs in smooth motion, the quintessence of an athletic ideal worshipped by Victorian men who aspired to be physical specimens worthy to rule an empire - yet this pristine example of the classical body was, in reality, used by the emperor Hadrian as part of a personal homosexual cult.

The deconstruction, however, is redundant. Such ironies never were lost on the artists and intellectuals who revived the Greek nude, again and again, across millennia - not on the Romans, nor on Renaissance artists, nor on Winckelmann, who died, it was said, in a homosexual encounter. How could anyone miss the reality of what Greek art was? Sex between men was endorsed by naked sports, all-male dinner parties and the comradeship of citizen armies. The Greek appetite for portraying the naked male body was a direct expression of a culture we would call homoerotic. The complexity comes when later Europeans emulate the Greek nude.

The question is - why did they want to? Why did European artists, again and again, turn to the classical depiction of the male body that had reached its apogee in Athens and other Greek city states in the 5th century BC, not merely as one interesting artistic theme, but as the single most serious subject in art? It was because the Greeks turned the body into philosophy.

Look at Greek depictions of the masculine figure and you soon see how regular, systematic and abstract they are: look at a nude torso painted on an Athenian vase, the black lines that define pectoral muscles with a crisp idealism. The same bold summary of the way a man's body should look - rather than any attempt to convey how a specific one looks - gives Greek statues a noble unreality. If you had to find a modern analogy for the oval definition of the groin in a statue by the 5th-century BC sculptor Polykleitos, it would not be any real body, but Action Man. This insistence on the true and permanent "ideal" body parallels the Greek philosophers and scientists, from Pythagoras to Plato, who sought the truth beyond visible appearances.

The Canon of Polykleitos - a book in which he analyses the correct proportions of the body - is lost, but the belief in a set of ideal proportions for the head, torso and limbs of a man survived into the Renaissance in the writings of the Roman architectural theorist Vitruvius. In the 15th century, Leonardo da Vinci drew his famous diagram of "Vitruvian man", arms and legs spread in a star shape, revealing that he fits inside a geometrical figure: there is a secret geometry in the human design.

Suddenly we can see, after all, what artists and art lovers in the past so revered about Greek statues and what they were talking about when they spoke of a classical ideal. They weren't just covering up unacknowledged desires. Leonardo's Vitruvian man does not strike us as erotic at all, but cosmological. The star shape the man assumes makes us see humanity on a mind-expanding, astral scale.

The strain - and it has been highly productive - in depicting the nude comes when it is revived by cultures nothing like as relaxed about the male body as Greece had been. The Greeks were well aware of the potential dangers of nude art - but this worried them only when it came to portraying women nude. When Praxiteles sculpted a fully naked Aphrodite, it was a sensational event. Pliny the Elder reports that visitors to her shrine couldn't contain themselves, and the stains of one man's encounter with the statue could still be seen in his day.

In Renaissance Italy, Plato's writings, in which male desire for men is a noble part of philosophical culture, were translated and revered, yet this was, nevertheless, a Christian society in which you could be burned for sodomy. Instead of making Renaissance artists timid before the male nude, the added frisson of sinfulness and punishment seemed to incite them.

Excitement still hangs in the air, like a fierce perfume, around Donatello's David in the Bargello Museum, Florence. This was a revolutionary work when it was cast in bronze in the middle of the 15th century, and it lives to this day as a confounding image. David wears leg armour that sets off his nudity. His buttocks are emphasised. The bronze of an adolescent, hand on hip, huge sword in his hand, is mounted on marble and you walk right around him, painfully aware of the sensuality of the polished metal.

The reason this is a far more troubling object - challenging you to account for your own response, whatever you think your sexuality is - has to do with style. Greek athletes are abstract. Donatello's David is vividly and unmistakably studied from a living model: instead of being regularised in Action Man contours, his body is supple and animated, a real body, from bellybutton to kneecaps.

Donatello's nude stood in the courtyard of the Medici Palace, announcing the spectacular return of the nude to art after a millennium of Christian guilt. Its naturalism inaugurates a completely new cult of the nude that takes inspiration from the classical ideal yet is aggressively realistic. This earthiness gives the Renaissance nude a passionate charge. Italian Renaissance art, as was once said of Burt Lancaster, is neither homosexual nor heterosexual but sexual, period. And this hypersexuality is intensified by Christian fear.

Renaissance nudes meet that fear with violence, as if punishing the male body to chastise the sin of looking at it: Saint Sebastian is a favourite - speared by arrows. And Christ crucified. In Caravaggio's Deposition in the Vatican, the naked flesh of Jesus is lowered into the tomb. The nude has become unheroic, pitiful, and human.

In one of Steven Meisel's photographs for Dolce & Gabbana, a naked man lies on the floor as if hurled down. In fact, this nude is taken from Caravaggio's painting of the conversion of Saint Paul, in Santa Maria del Popolo in Rome, the saint thrown on to his back by the force of divine truth. In the Dolce & Gabbana ad, this image of anguish and revelation becomes more provocative than harrowing. The tensions that were so creative in Renaissance art fade.

The modern urge to define and map sexuality, to make knowledge of sex specific and categorical in a way it simply was not for Donatello, may have made us happier. It has not made us more imaginative. The unresolved way in which previous centuries contemplated the male body produced (to quote Orson Welles in a different context) "Michelangelo, Leonardo da Vinci and the Renaissance". What have we produced? The thong.