However, the chance discovery of a letter by an archaeologist researching a book led to the skeleton's re-discovery in the Natural History Museum.
The skeleton was unearthed in 1923 but was thought to have been destroyed in 1941 by the Nazi bombing blitz on London. At that time, it was being held at the Royal College of Surgeons, which suffered three direct hits.
However, the chance discovery of a letter by an archaeologist researching a book led to the skeleton's re-discovery in the Natural History Museum.
Modern analysis techniques show that the skeleton belonged to a man aged about 35 who had his head cut off by a sword.
The man may have died 2,000 years ago, and it had been thought that his death was the result of natural causes.
Clean cut
However, Jacqueline McKinley, of Wessex Archaeology, discovered a small nick on the lower jaw and a cut mark on the fourth neck vertebra.
This clean cut from behind, and his single grave, suggest an execution with a sharp sword, rather than a death in battle.
English Heritage, who manage Stonehenge, said: "Why he was executed is not known. But it is possible that he was singled out for special punishment, as Stonehenge clearly represents a dramatic and important site for the event."
It was thought that Stonehenge, built in three phases between 3050BC and 1600BC, was abandoned by 1500BC. But this evidence suggests the site retained importance centuries later.
Rare find
David Miles, Chief Archaeologist at English Heritage, said: "Stonehenge is a site of global significance and anything that adds to our knowledge and understanding is of great importance."
Only one other complete skeleton from Stonehenge exists. It was excavated in 1978 from the ditch around the circle. The man had died in a hail of flint-tipped arrows.
Two other skeletons have been found. One was probably a Roman, and was reburied at Stonehenge in 1922. The other was excavated in 1926 from the centre of the circle and was possibly contemporary with the site, but has now been lost.
