It is in Botero's pictures with religious subject matter that the reminiscences of his earliest confrontations with visual imagery are most strongly recalled. In the churches that Botero's family would attend in Medellín as well as in the small country town of El Escorial, where they would spend part of the summer, carved wood images of the Virgin, the saints and Christ formed the principal adornment. Derived from the Spanish polychrome tradition of sculpture, these images were as substantially realistic as possible, equipped not only with real-looking paint to define the facial features, but with clothing, human or animal hair on their heads, and glass eyes, to make them even more palpable presences among their worshippers. In addition, the colonial paintings that adorned the side and the principal altars featured similar characteristics of exaggerated 'realness' fused with a Baroque devotion to decorative detail.The innocent piety and absolute faith in the potency of spiritual proximity embodied by these images are equally evoked by many of the paintings of saints and the Virgin Mary done throughout Botero's career. It is important to note an essential difference, however. Although Botero does not subject his religious images to the test of irony or scepticism, his paintings and drawings are not done with the same sense of unquestioning faith as those from which he derived inspiration. Botero's position is always that of a late twentieth-century artist revisiting religious subject matter, completely aware of the gulf that exists in our time between blind faith in religious doctrine and the inevitable doubts imposed by the secular world of today.

The quintessential image of this category is Our Lady of Colombia of 1967, which is, appropriately enough, in the collection of the Museo de Antioquia in the artist's home town of Medellín. Reminiscent of the "statue paintings" (images that depict the Baroque sculptures of the Virgin located in niches and on altars) of the Cuzco school of Peru and Bolivia, the crowned Virgin stands before an aureole decorated with roses. She holds the Christ Child (who Himself holds a tiny orb and the Colombian flag) in one arm and a scapular in the other.

Botero also refers to a specific South American sense of religiosity in his depictions of Saint Rose of Lima, such as the 1978 example in which the first American saint wears a halo of roses. More roses float in the air around her Even in his much later work, he continues to refer back to South American pictorial traditions. A 1995 painting entitled Angel with Red Hot (one of several large-scale compositions of this subject), in which we observe a Guardian Angel figure standing on the rooftops of a small Colombian village, is a re-consideration of another archetypical subject in South American colonial painting. Angels holding guns were depicted hundreds of times in Peruvian and Bolivian colonial images representing paradigms of the militant Catholic faith. These angels may also be comprehended as symbols of Catholicism triumphant over indigenous religions.

At the opposite side of sanctity is damnation, and in Botero's imagination the devil plays as dramatic (and much more humorous) a role as do the Virgin, Christ and the saints. Botero's visions, such as the 1978 Hell, may attempt to conjure up analogous feelings of dread as those of, say, Hieronymus Bosch, but they never quite succeed in making us believe in the incendiary powers of eternal flames.