When James Tyrrell was tortured into confessing to the murder of the Princes in the Tower, he seemed to have trouble locating where precisely they were living at the time.
We know that they were in the north-eastern (round) turret of the White Tower. He claimed that he buried their bodies under the stairwell of the Bloody Tower.
This left a bit of a plot hole in the story, which generations of historians have scurried to fill. Alison Weir, for example, has the princes willingly walking over to the Bloody Tower from the White Tower, on a promise of meeting up with their mother, if they're good and quiet.
Tyrrell's tale nevertheless received a great boost in 1674. As part of a huge renovation project on behalf of the Stuarts, workman set about 'pullinge down the Tower against the White Tower'. This was almost certainly the twelfth century fore-building, which had been allowed to be constructed against the south wall. Most agreed that it was not only ugly, but hindered the defense of the White Tower.
As the 17th century demolition crew moved in, they made a grisly discovery. Under the flagstones of the corridor leading into the chapel were the skeletal remains of two children.
Charles II promptly declared them the Princes in the Tower and had an ornate urn sculpted to receive their bones. It still sits in Westminster Abbey, labelled Edward V and Richard, Duke of York.
Scientists got to have a peep at the skeletons in 1933. They determined that some of the bones actually belonged to chickens and the like, but there were definitely two children of roughly the right ages in there. The gender could not be discerned.
(It could now, but Queen Elizabeth II refuses permission for modern forensic experts to open the urn.)
All cut and dry, Princes found and all that. Except for two small details. Why aren't they where James Tyrrell said that he left them? (The semi official explanation is that they were moved from the Bloody Tower to the White Tower after Tyrrell left.) And, if they are the Princes, then who is buried in the crypt in Windsor with their parents?