Scientists are now analyzing the human remains to try to learn more about the identity of those who died.
The battle was fought near Waterloo village, south of Brussels, on June 18, 1815. Napoleon Bonaparte was finally defeated here by the Duke of Wellington's combined Allied army of 68,000, aided by 45,000 Prussians under Gebhard von Blücher.
While more than 10,000 men are believed to have died during the battle, only two bodies have ever been discovered.
Historians recently revealed that many of those who fell at Waterloo were later dug up by farmers, who sold their remains to the sugar industry for use in the industrial process.
Last November, Bernard Wilkin, a senior researcher at the State Archives of Belgium, was in Waterloo giving a talk on the process -- in which the bones used as a kind of charcoal in sugar purification -- when something astonishing happened.
After the talk, he told CNN, "this old man came to me and said 'Dr. Wilkin, I have bones of these Prussians in my attic.'"
The man, who wishes to remain anonymous, showed Wilkin pictures of the bones and invited him to his house near the battle field in Plancenoit, where Napoleon's forces faced off against the Prussians.
A few days later, Wilkin visited the man at his home and came face to face with the remains, which the man had had since the 1980s. He explained that he ran a "small private museum" at the time and was given the remains for display by a friend who had found them some years earlier..
Despite being a collector of Napoleonic memorabilia, the man told Wilkin he could not "ethically" bring himself to display the remains, so stored them away in his attic.
Wilkin said of the man, who lives alone: "He suddenly decided he was old and could pass away in the next years and he was afraid of what would happen to the bones. When he saw the research we released last summer he thought 'this guy knows about bones and the Napoleonic wars and he works for the government.'"
Wilkin said he felt a "mixture of surprise and emotion" when he saw the remains.
"One of the skulls is deeply damaged by a sword or a bayonet, so it was a very brutal way of dying," he said.
Initial tests revealed that the remains belonged to at least four soldiers. Items found close to the bones, including leather and bone buttons, as well as the location in which they were discovered, suggested some of the dead were Prussian soldiers.
Wilkin said: "At the end of the day he gave me all the boxes to study. One of his requests to me was to bury them in a dignified way."
That is certainly the plan, but for now the remains are undergoing extensive forensic testing in Liège, where Wilkin is based. Scientists hope to extract DNA in a bid to identify the dead. They also hope to make facial reconstructions of at least one of the skulls.
Rob Schäfer, a German military historian, is working with Wilkin to try to learn more about the soldiers, while also liaising with the German War Graves Commission.
He told CNN: "What fascinated me most is the fact that if you look at art from the 19th century, where conflict is depicted, it's all very interesting and abstract. As a casual observer you might get the impression it wasn't that bad, but this one particular skull with a massive facial trauma depicts for the first time how violent the age actually was."
Schäfer told CNN there is a 20%-30% chance of extracting DNA from the remains.
He said: "It's a long shot but if we're successful, the next goal is to load the DNA on to databases so people could come forward if they found they were related."
After encountering the bones in the attic, there was a further surprise in store for Wilkin.
"When I was visiting, the man told me 'by the way, I have another friend who has probably four British soldiers that he discovered while (metal) detectoring next to the Lion's Mound (on the battle field)," he said.
"I was taken aback, this was getting really crazy."
Wilkin told CNN that those bones were later examined by Dominique Bosquet, an archaeologist from the Walloon Heritage Agency. They have since been moved to Brussels, where they are being studied by Bosquet and a team from the Natural History Museum and the University of Brussels.
The finds have led Wilkin and his colleagues to suspect that more people living close to the battlefield may have skeletons in their closets.
"It's quite clear that we need to talk to the people who have lived there for generations," he said, adding: "We are pretty sure that more bones need to be given back to the Belgian authorities."
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