Wednesday, July 21, 1999 Published at 18:34 GMT 19:34 UK
The Kennedy search in pictures
He was flying with his wife Carolyn and her sister Lauren Bessette from New Jersey to Massachusetts.
But the rescue operation soon turned into a search for bodies.
From the moment the young John F Kennedy Jnr saluted his assassinated father, he won a special place in the nation's heart. His progress through life was always closely monitored.
Within hours of the news breaking that his plane had disappeared, a number of sites - including Mr Kennedy's family home in New York - became impromptu memorials.
Part of the search was carried out on land, as debris was washed ashore at Aquinnah Beach, Massachusetts.
From the air, spotter planes scoured the ocean for clues to the crash site.
And at sea, divers and sonar equipment were used to find the wrecked fusilage of the Piper Saratoga, which was carrying Mr Kennedy and his two passengers.
Among the debris washed ashore was a travel bag and one of Lauren Bessette's business cards.
Robert Kennedy Jnr and his wife Mary joined other relatives at Hyannisport, Mass, to wait for news.
But before any bodies were found, the Kennedy clan had acknowledged another tragic loss and lowered the Stars and Stripes to half mast.