"Here lie the relics of Edward V, King of England, and Richard, Duke of York. These brothers being confined in the Tower of London, and there stifled with pillows, were privately and meanly buried, by the order of their perfidious uncle Richard the Usurper; their bones, long enquired after and wished for, after 191 years in the rubbish of the stairs (those lately leading to the Chapel of the White Tower) were on the 17th day of July AD 1674 by undoubted proofs discovered, being buried deep in that place. Charles II, a most compassionate king, pitying their severe fate, ordered these unhappy princes to be laid amongst the monuments of their predecessors, AD 1678, in the 30th year of his reign."

In 1789, workmen carrying out repairs in St George's Chapel, Windsor, rediscovered and accidentally broke into the vault of Edward IV and Elizabeth Woodville. Adjoining this was another vault, which was found to contain the coffins of two children. This tomb was inscribed with the names of two of Edward IV's children: George, 1st Duke of Bedford, who had died at the age of 2; and Mary of York who had died at the age of 14. Both had died before the King. However, the remains of these two children were later found elsewhere in the chapel, leaving the occupants of the children's coffins within the tomb unknown.

Edward and his brother Richard's fate after their disappearance remains unknown, but the most widely accepted theory is that they were murdered on the orders of their uncle, King Richard. Thomas More wrote that the princes were smothered to death with their pillows, and his account forms the basis of william Shakespeare's play Richard III, in which Tyrrell murders the princes on Richard's orders. Subsequent re-evaluations of Richard III have questioned his guilt, beginning with william Cornwallis early in the 17th century. In the period before the boys' disappearance, Edward was regularly being visited by a doctor; Historian David Baldwin extrapolates that contemporaries may have believed Edward had died of an illness (or as the result of attempts to cure him). In the absence of hard evidence a number of other theories have been put forward, of which the most widely discussed are that they were murdered on the orders of the Duke of Buckingham or by Henry Tudor. However, Pollard points out that these theories are less plausible than the straightforward one that they were murdered by their uncle who in any case controlled access to them and was therefore regarded as responsible for their welfare. An alternative theory is that Perkin Warbeck, who claimed to be a pretender to the throne, was indeed Richard of Shrewsbury, Duke of York as he claimed, having escaped to Flanders after his uncle's defeat at Bosworth to be raised with an aunt.