The scientist, who is the co-founder of Lumiere Technology in Paris, was given access to the painting in 2004 by the Louvre.
He has pioneered a technique called Layer Amplification Method (LAM), which he used to analyse the Mona Lisa.
But Mr Cotte has claimed his discoveries challenge that theory. He believes the image he has reconstructed underneath the surface of the painting is Leonardo's original Lisa, and that the portrait named Mona Lisa for more than 500 years is, in fact, a different woman.
He said: "The results shatter many myths and alter our vision of Leonardo's masterpiece forever.
"When I finished the reconstruction of Lisa Gherardini, I was in front of the portrait and she is totally different to Mona Lisa today. This is not the same woman."
He also claims to have found two more images under the surface of the painting - a shadowy outline of a portrait with a larger head and nose, bigger hands but smaller lips. And he says he has found another Madonna-style image with Leonardo's etchings of a pearl headdress. Source: BBC