They found two young boys skeletons under stairs when renovating the tower. The Queen, so far, refuses to allow testing to determine if they are the two young Princes who rumors indicate were smothered on their Uncle’s orders. It is almost 100% these two young Princes. Who else would be disposed of under stone stairs in the Tower?
Some of the oldest versions of the story specify that the two boys were killed and buried under some stairs. But they also say that the bodies were then moved to another location and reburied. In 1674, some bones were found under a stairway in the White Tower and it was assumed these were the princes. The bones were put into an urn and placed in Westminster Abbey. In 1933 these bones were examined. Many bones were missing and they were mixed with animal bones. Jawbones were consistent with the ages of the princes. The bones were returned to the urn and have not been examined since.
In 1798, workmen accidentally broke into a tomb and found two unmarked coffins, but the tomb itself had the names of two of Edward IV's other children, who had died of natural causes during his reign. In the 1990s, there was an effort to convince the queen to allow these coffins to be opened and examined, but she didn't grant the request.