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The young lad screams while his head is firmly held, a massive digit pressing into his face as his parent's powerful hand holds him by the throat. This scene from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through the artist's chilling portrayal of the suffering youth from the scriptural account. It appears as if the patriarch, instructed by God to sacrifice his son, could snap his spinal column with a solitary twist. Yet Abraham's chosen method involves the metallic grey blade he holds in his remaining hand, prepared to cut the boy's throat. A certain element remains – whomever posed as Isaac for this breathtaking work displayed remarkable acting ability. There exists not only fear, shock and pleading in his darkened eyes but additionally deep sorrow that a protector could abandon him so completely.

The artist took a well-known scriptural tale and transformed it so fresh and raw that its terrors appeared to happen right in front of the viewer

Standing before the artwork, observers recognize this as a real countenance, an accurate depiction of a young subject, because the identical boy – recognizable by his disheveled locks and almost dark pupils – features in several additional paintings by Caravaggio. In every case, that richly emotional face commands the composition. In John the Baptist, he peers mischievously from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his dark feathery wings sinister, a naked child running riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a British museum, constitutes one of the most discomfiting artworks ever created. Observers feel totally unsettled gazing at it. Cupid, whose arrows inspire people with frequently painful longing, is portrayed as a extremely real, vividly lit unclothed figure, standing over toppled-over items that include stringed instruments, a music score, metal armour and an builder's T-square. This heap of possessions echoes, deliberately, the mathematical and construction gear strewn across the floor in the German master's print Melencolia I – except in this case, the melancholic disorder is created by this smirking Cupid and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted sightless," wrote Shakespeare, just prior to this painting was created around 1601. But Caravaggio's Cupid is not unseeing. He stares straight at you. That face – ironic and rosy-cheeked, staring with bold confidence as he poses naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the identical unusual-looking youth in Rome at the dawn of the seventeenth century, he was the most acclaimed religious artist in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could take a biblical story that had been portrayed many occasions previously and render it so new, so unfiltered and physical that the horror seemed to be happening immediately in front of you.

However there existed a different aspect to the artist, apparent as soon as he arrived in the capital in the cold season that ended 1592, as a painter in his early twenties with no teacher or patron in the urban center, only talent and boldness. Most of the works with which he caught the sacred city's eye were everything but holy. That could be the very earliest resides in London's art museum. A young man opens his red lips in a scream of agony: while stretching out his dirty digits for a cherry, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can see the painter's dismal chamber reflected in the cloudy waters of the glass container.

The adolescent sports a rose-colored blossom in his coiffure – a emblem of the sex trade in early modern painting. Northern Italian painters such as Titian and Jacopo Palma portrayed courtesans grasping flowers and, in a painting destroyed in the WWII but documented through images, Caravaggio represented a famous female prostitute, holding a bouquet to her bosom. The meaning of all these floral indicators is obvious: sex for sale.

What are we to interpret of the artist's erotic portrayals of boys – and of a particular adolescent in particular? It is a inquiry that has divided his interpreters ever since he gained widespread recognition in the twentieth century. The complex past truth is that the artist was neither the queer icon that, for instance, Derek Jarman presented on film in his twentieth-century film Caravaggio, nor so entirely pious that, as some art historians unbelievably claim, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early works indeed offer overt sexual suggestions, or including propositions. It's as if the painter, then a destitute youthful artist, aligned with Rome's sex workers, offering himself to survive. In the Uffizi, with this idea in mind, viewers might turn to another initial work, the sixteenth-century masterwork the god of wine, in which the god of alcohol stares coolly at the spectator as he begins to undo the dark sash of his garment.

A several years after Bacchus, what could have motivated the artist to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was at last growing almost respectable with important church commissions? This profane non-Christian deity resurrects the sexual provocations of his initial paintings but in a more powerful, uneasy way. Fifty years later, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British traveller viewed the painting in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The name of this adolescent was Cecco.

The artist had been dead for about forty annums when this account was documented.