Reuters is reporting that the discovery of the demon was made by Chiara Frugone, a medievalist and expert on St. Francis, who found it in the detail of some clouds that appear at the top of one of the frescos that portrays the death of St. Francis.
Although it's difficult to make out the image from the floor of the basilica, it is clearly discernable in close-up photography.
"It's a powerful portrait, with a hooked nose, sunken eyes and two dark horns," Ms Frugoni said in an article in a forthcoming issue of the St Francis art history periodical.
"The significance of the image still needs to be delved into. In the Middle Ages it was believed that demons lived in the sky and that they could impede the ascension of human souls to Heaven."
Sergio Fusetti, the chief restorer of the basilica, speculated that the artist may have painted the figure in the clouds "to have a bit of fun" or to spite someone he knew by portraying him as a devil.
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Photo of fresco is by Reuters.