"They were much smaller than human baby hands, and the fingers were too long," she told National Geographic.
The scientists took measurements of the stencils and compared them to those of newborn human infants under a year, including newborn premature babies that were 26 to 36 weeks old.
But came to the startling conclusion that the prints were not human and instead were created by lizards.
But while Honoré is sure the prints were made by tiny crocodiles or lizards - she is unsure of the reason why they are there.
Or why any civilisation would want to draw or use the legs of animals on their cave walls.
She added: "It's very challenging for us as researchers to interpret these paintings since we have a culture that's totally different."
Situated in the Eastern Sahara, the Cave of Beasts is six miles from the renowned Cave of the Swimmers but it contains some of the most incredible archaeological images ever found.
The dessert is the world's largest and is the size of Western Europe and goes from Egypt into Libya, Sudan and Chad.
It is one of the driest places on earth - but wouldn't have necessarily been so when the images were made - since there would have been water to sustain life.