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The young boy screams as his head is firmly held, a massive digit digging into his cheek as his parent's powerful hand grasps him by the neck. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's chilling portrayal of the suffering child from the scriptural account. The painting appears as if Abraham, instructed by the Divine to sacrifice his son, could break his neck with a single twist. Yet the father's preferred method involves the silvery grey blade he grips in his remaining hand, ready to cut Isaac's neck. A certain aspect remains – whoever posed as Isaac for this breathtaking piece displayed extraordinary acting ability. Within exists not only dread, surprise and pleading in his darkened eyes but also deep grief that a guardian could abandon him so utterly.

He took a familiar scriptural story and transformed it so fresh and visceral that its terrors seemed to unfold directly in front of you

Standing before the artwork, observers identify this as a actual face, an precise depiction of a adolescent model, because the identical youth – recognizable by his tousled locks and nearly dark eyes – appears in several other paintings by Caravaggio. In every instance, that highly emotional face commands the scene. In John the Baptist, he peers playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's alleys, his black plumed appendages demonic, a unclothed adolescent running chaos in a affluent dwelling.

Victorious Cupid, presently displayed at a London museum, constitutes one of the most embarrassing artworks ever created. Observers feel totally unsettled gazing at it. The god of love, whose darts fill people with frequently agonizing desire, is shown as a very real, brightly illuminated unclothed figure, straddling overturned items that include musical instruments, a music score, plate armor and an architect's ruler. This heap of possessions resembles, intentionally, the geometric and construction gear strewn across the floor in the German master's engraving Melancholy – save in this case, the gloomy mess is created by this grinning deity and the turmoil he can release.

"Affection looks not with the vision, but with the soul, / And thus is winged Love painted blind," penned Shakespeare, shortly before this work was created around the early 1600s. But Caravaggio's god is not blind. He gazes directly at the observer. That countenance – ironic and ruddy-cheeked, looking with brazen assurance as he poses unclothed – is the identical one that shrieks in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three images of the same unusual-appearing youth in Rome at the start of the 17th century, he was the most acclaimed religious artist in a city ignited by religious revival. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could adopt a scriptural story that had been portrayed numerous occasions before and make it so fresh, so raw and visceral that the horror seemed to be occurring directly in front of the spectator.

However there was a different aspect to the artist, evident as quickly as he arrived in Rome in the winter that ended the sixteenth century, as a artist in his initial 20s with no mentor or supporter in the city, only talent and audacity. The majority of the paintings with which he caught the holy city's eye were everything but devout. What could be the absolute earliest hangs in the UK's National Gallery. A young man opens his red mouth in a yell of pain: while reaching out his filthy fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern the painter's gloomy room mirrored in the cloudy liquid of the glass container.

The adolescent wears a pink blossom in his coiffure – a symbol of the erotic trade in Renaissance painting. Venetian artists such as Tiziano and Jacopo Palma depicted courtesans grasping flowers and, in a work destroyed in the WWII but documented through images, the master represented a famous female prostitute, clutching a posy to her chest. The meaning of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of the artist's erotic portrayals of boys – and of one adolescent in particular? It is a inquiry that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complicated historical reality is that the artist was not the homosexual icon that, for example, Derek Jarman presented on film in his twentieth-century film Caravaggio, nor so entirely devout that, as certain artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works indeed make explicit erotic implications, or even propositions. It's as if the painter, then a penniless youthful artist, aligned with Rome's sex workers, selling himself to survive. In the Uffizi, with this thought in consideration, observers might look to another initial work, the sixteenth-century masterpiece Bacchus, in which the deity of wine stares calmly at you as he begins to undo the dark ribbon of his robe.

A several years following the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally growing almost established with important ecclesiastical commissions? This unholy non-Christian god resurrects the sexual challenges of his initial paintings but in a more intense, unsettling manner. Fifty years afterwards, its hidden meaning seemed obvious: it was a representation of Caravaggio's lover. A English traveller viewed the painting in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this boy was Francesco.

The artist had been deceased for about forty annums when this account was recorded.