Bones from 18 bodies have been discovered by Durham University experts during building work at the Palace Green Library, part of the World Heritage Site in the city centre.
It was thought the bodies were buried in the cathedral's medieval cemetery which was bigger than the current burial plot.
But further examination revealed an unorthodox and intriguing layout to the bodies which archaeologists say is proof of a mass burial.
Richard Annis, senior archaeologist said: "The bodies have been tipped into the earth without elaborate ceremony and they are tightly packed together and jumbled.
"Some are buried in a North to South alignment, rather than the traditional East to West alignment that we would expect from a conventional medieval burial site."
Mr Annis says that it is too early to say what they may be. Further research will be carried out in the New Year.
Once the bones have been examined - with permission from the Ministry of Justice - they must be reinterred at an approved burial ground.