The theory presented by a renowned art historian Dr Ross King suggests Leonardo used his own face for two of the apostles.
King believes he has uncovered new evidence that the master artist inserted himself not once, but twice, into his famous mural, The Last Supper.
King, the author of the international best-seller Brunelleschi's Dome, makes reference to a poem written in the 1490s, while Leonardo was painting The Last Supper, by his friend Gasparo Visconti.
Visconti makes fun of an unnamed artist in the poem for putting his image into his works "however handsome it may be".
King also cites the famous portrait of a man in red chalk, sketched around 1515 AD, which is thought to show Leonardo in his advancing years.
King gives a reference to a portrait believed to be of da Vinci in his later years showing him with a Greek nose and flowing hair, much like the two apostles.
More From This Section
Thomas is also pointing his finger upwards in the 500-year-old mural, a gesture which Leonardo's contemporaries viewed as a da Vinci trademark.
"The Last Supper is the only work that no one, either crackpot or academic, has tried to identify as a Leonardo portrait," Dr King told 'the Independent'.
In his book, Dr King writes that "Leonardo spotting has become a popular pastime" with numerous identifications.
"Of all the apostles that [Leonardo] would wish to be identified with, I think Doubting Thomas would be top of his list because Leonardo was a great believer in asking questions rather than accepting what people tell you," Charles Nicholl, the noted Leonardo scholar, said.
Leonardo is the man behind some of the most famous portrait paintings in history, however art experts still have relatively little idea what he himself looked like.
Because the Renaissance genius left no self-portraits from his youth, academics have been suspect that he may have placed his image into one of his own masterpieces.
The Last Supper was painted on an end wall in the dining hall at the monastery of Santa Maria delle Grazie in Milan, Italy, for Leonardo's patron Duke Ludovico Sforza and his duchess Beatrice d'Este.