Dave Duerson had so much going for him. A former professional American football player, he still carried himself with the bearing of a star. In Chicago, he was feted as a member of the legendary 1985 Bears that won the Super Bowl, thrashing the New England Patriots 46-10. In New York, too, he was fondly remembered as a member of the Giants team that took the Super Bowl championship five years later, squeaking to victory over the Buffalo Bills by just one point.

He had friends throughout the sport, acquired over an 11-year career with the National Football League (NFL) and many years subsequently helping younger and less fortunate players find their way. He had a loving family with three sons and a daughter and a former wife, Alicia, who kept in regular touch, as well as a girlfriend to whom he had recently become engaged. He lived in a condominium that he owned on Sunny Isles Beach in Florida, a barrier island close to Miami dubbed the Venice of America. He was smart, charming, as kind and gentle off the field as he had been aggressive and ruthless on it.

But he knew that he had a problem. There were the outward signs of difficulties – the collapse of his business, the breakup of his marriage, the debts. But there were also the internal changes. The lapses in memory, the mood swings, the piercing headaches on the left side of his head, the difficulty spelling simple words, the blurred eyesight. And hanging over it all was his fear that both his material and physical decline might not be coincidental, that they might have been caused by injuries to his brain suffered playing the game he loved so much – football.

On 17 February 2011, aged 50, Duerson killed himself inside his Florida apartment. He did so in a manner that was in keeping with his unimpaired earlier self – meticulously, neatly, and with a thought to others. He had placed his NFL Man of the Year trophy, awarded in 1987, on a table beside the spot at which he fell, along with several notes setting out his financial and other arrangements. One of the notes carried a request that he repeated in a text message earlier that day to his ex-wife, Alicia. "Please, see that my brain is given to the NFL's brain bank," he said.

The request might have been deemed a quirk had it not tallied with the unusual method of Duerson's suicide. He shot himself in the heart.

* * *

The Center for the Study of Traumatic Encephalopathy – a research facility so clunkily named that it's unsurprising Duerson used a semi-accurate abbreviation, "the NFL's brain bank" – sits in the pleasantly green and airy grounds of the Bedford VA medical centre in Massachusetts, about an hour's drive outside Boston. It was set up three years ago by concerned former athletes who joined forces with Boston University scientists to grapple with the long-term effects of concussions on sportsmen and women, soldiers and other people subjected to brain injuries.

Security is tight as you enter the building through heavily bolted metal doors. We pass rooms lined with shelves of jars carrying human brains pickled in formaldehyde. At the end of a corridor, we arrive at a small room into which several stainless steel refrigerators have been packed, one of which is marked: "Feet first. Head by door."

In this morgue the world's largest bank of athletes' brains is being stored on dry ice. It has grown exponentially in the past couple of years to include 75 brains, mostly of American football players but also of hockey enforcers – the tough guys who do the bare-knuckle fighting – and of former soldiers caught in bomb blasts. A further 400 living athletes have promised to donate their brains upon death, including some of the biggest names in their sports. They include "Irish" Micky Ward, the boxer played by Mark Wahlberg in the film The Fighter, and American footballers Matt Birk (Baltimore Ravens), Lofa Tatupu (Seattle Seahawks) and Sean Morey (Arizona Cardinals).

Neuropathologist Dr Ann McKee, a leading expert on degenerative diseases caused by repetitive blows to the head, looks at the brain of an American football player who recently died guardian.co.uk

Dr Ann McKee, a neuropathologist who jointly heads the lab, retrieves a brain from a plastic container and places it carefully on a workbench. At the request of the family, she will not tell me who the brain belonged to, other than to say "he was a very skilled NFL player, very well known".

If you were a fan of American football, I ask her, would you know the name?

"Right," she replies.

McKee is a world expert on chronic traumatic encephalopathy, or CTE, a progressive degenerative disease similar to Alzheimer's in its symptoms – memory loss, irritability, mood changes – but with its own distinct pathology. The disease has long been recognised: it was first described in 1928 and for many years was thought to be confined to boxers, hence the name "punch drunk" syndrome or "dementia pugilistica". But in the past three years, largely as a result of the work of McKee's brain bank, it has come to be seen as a danger to anyone who suffers repetitive concussions.

McKee begins her examination of the unidentified football star's brain by turning it in her surgically gloved hands with the tender concentration of a fruit-lover inspecting a pineapple. "It's too small for an adult male's brain," she says. "There's shrinkage pretty much throughout the brain."

Using a long knife, she cuts the organ sideways – from ear to ear, as it were – so that the front half is separated from the back. The sliced surface glistens under the morgue's neon lighting.

The dissection reveals three huge holes in the brain – one large triangle right in the centre of the brain, and two ovals parallel to each other at the base. It is apparent that McKee, who has studied more athletes' brains than probably any other person, is shocked by what she sees.

"This is an extreme case," she says, "but it is also very characteristic." She points to the triangular hole, consisting of the lateral ventricles, and says it clearly shows "tremendous disruption". There should be a membrane separating the two ventricles, but it has been so battered by the footballer's repeated blows to the head that only the thinnest of filaments is left. The two oval holes are the ventricles of the temporal lobe and they too are extremely enlarged to compensate for tissue lost from the lobes themselves, another classic sign of having your head bashed repeatedly. "The temporal lobes are crucial to memory and learning and you can see they are very, very small, as miniaturised as possible."

McKee takes a deep look at the cross-section of this brain and momentarily appears sad. "This is a brain at the end-stage of disease," she says. "I would assume that with this amount of damage the person was very cognitively impaired. I would assume they were demented, had substantial problems with their speech and gait, that this person was Parkinsonian, was slow to speak and walk, if he could walk at all."

Without being melodramatic about it, I say, you are holding in your hands an example of the price that is paid for being a professional footballer at the top of his game.

She hesitates a second. "At least in this case, yes," she says.

* * *

As a kid, Duerson was an exceptional all-round sportsman who could have pursued a career in baseball or in basketball. But it was football that he loved best. He started playing the game aged eight and carried on through school and into the celebrated football college, the University of Notre Dame in Indiana, picking up numerous awards along the way. He had 24 full seasons before he hung up his boots.

He tended to play strong safety, a key position at the back of the team that is the last line of defence. He would be lined up against the big offensive players on the opposing side, men who can weigh 300lb and whose job it is to drive and grind their team forward. It was Duerson's job to stop them, even if that meant crunching head first into the human equivalent of a brick wall.

It was when he was playing for Notre Dame at the Sugar Bowl, the annual showcase of American college-level football in New Orleans, that he met his wife of 25 years, Alicia. She wasn't interested in football. But she was instantly struck by him the first time she saw him at a party.

"Dave could walk in and capture a room. He had a lot of charisma, he had a lot of magic to him. He was 6ft 2in, but the way he carried himself he seemed like a bigger guy," she says when we meet in Chicago.

They married in 1983 after he graduated with a degree in economics. He had thoughts of going to law school or entering politics, but the draw of a professional career in football proved irresistible and he was selected to play for the Chicago Bears that same year.

Alicia and their four children attended every game. It was hard watching him take a battering in such a physical contact sport, but he was tough and competitive and she comforted herself that it was usually Duerson who delivered the pounding. "He wasn't taking the hits, so much as giving them out."

But over the 11 years he played as a professional, the family can recall at least 10 concussions that he suffered on the pitch. That's the bare minimum, as he may have had many other knocks to the head that weren't registered.

"He never came off the field and would always continue to play, so a lot of times I wouldn't learn 'til after the game," Alicia recalls. Duerson would tell her: "I took a strong hit to the head, I'm a little dizzy, let's drive home," and would try and shake it off.

"Back then it was a man's game," she says. "Gladiator. Ra, ra. He'd say he felt nauseous and need to rest, and go and lie down for a while." Within days, sometimes hours, he'd be back on his feet and back on the field.

For a long time, everything Duerson touched turned to gold. On top of his two Super Bowls, he was declared NFL Man of the Year in 1987 and NFL Humanitarian of the Year the following year.

After he retired from the game in 1993 the successes continued. He refreshed his economics degree with a business course at Harvard and entered the food business, purchasing three McDonald's franchises in Louisville, Kentucky, before setting up his own business, Duerson Foods, supplying sausages to chains.

When times were good, they were very good. They owned a house in Highland Park, a leafy town on the shore of Lake Michigan north of Chicago. They travelled the world, flying Concorde.

But from around 2005, almost a decade after he had given up football, their fortunes started to turn. It was such a slow process, like watching a child grow, that Alicia hardly noticed at first. It started with Duerson making bad business calls in a way that was unlike him.

"He was making hasty decisions. A lot of things that would come natural to him wouldn't any more. He started to lose his ability to function, to think things clearly through," Alicia says.

The business started to suffer, profits to fall and debts to mount. At the same time, Duerson himself began to decline. He had severe headaches with increasing frequency. He would have sharp mood swings, happy one moment, sad or angry the next. He would lash out verbally at those around him. Small things annoyed him, particularly his own inability to do simple things. He would get lost going to places he had been to umpteen times before, as his memory started to fail.

Then in February 2005 he was charged with assault after he attacked Alicia in a hotel room in Indiana; she had to have hospital treatment. They separated two years later. By then Duerson had lost everything, not just his marriage. Duerson Foods went bust and he went bankrupt. They had to surrender the house. The celebrity lifestyle that the Duersons enjoyed on the back of his NFL days had entirely vaporised. He took that hard. "David was so disappointed in himself," Alicia says. "He was a very proud person, and he couldn't handle the failure of it. We had built this beautiful life together, and he lost it all."

It took McKee about two months to carry out her investigation into Duerson's brain. The process involved taking many slices of crucial areas of his brain and staining them with a fluid that highlights the buildup of abnormal proteins. The slices are then turned into slides for microscopic study.

McKee pulls up photographs of the slides on her laptop. They look like images you might find on Google Earth showing a satellite picture of an island whose coastline is broken up with deep inlets. Much of the coastline and several of the inlets are stained a dark brown.

This indicates the presence of tau, an abnormal protein that forms in the brain as a result of a trauma or injury often caused by a blow to the head. McKee explains, the accumulation of tau in nerve cells clogs them up and eventually kills them, and over the years it can spread to neighbouring cells and shut them down too, progressively destroying the brain's function.

"This amount of damage in a 50-year-old is really profound, it's huge," McKee says, pointing to the brown inlets on Duerson's slide. "To show this degree of degenerative disease at that young age is quite extraordinary."

The areas of Duerson's brain in which she found the accumulations of tau matched perfectly Alicia's description of his deterioration: there was damage visible to the inferior and dorsal frontal lobes that are crucial in regulating impulsive behaviour, and in the amygdala, which controls emotions such as rage. "With this kind of injury I would expect the person to display exaggerated and at times assaultive responses," she says.

Duerson's fear, that so many years of taking blows to the head on the football field were catching up on him, was confirmed under the microscope. He did indeed have CTE at an advanced stage.

McKee stresses that Duerson's donation of his brain in a suicide note was not something that they would wish repeated in any way. It was a tremendous tragedy. "Our first and foremost concern is that in no way do we want this to happen to any other individual. There's actually great hope for people who are concerned about themselves – this is a very slow-progressing disease and our understanding of CTE is growing every day."

But the diagnosis helps understand why Duerson ended his life the way he did. Of the 50 cases that have so far been diagnosed as having CTE at the brain bank, no fewer than 10 of them killed themselves, while others died in strange and violent ways such as wild car chases, gun accidents or drug overdoses.

For Alicia Duerson, her former husband's diagnosis has given her some comfort. "I'm really glad for our kids, it's brought closure. Their father killed himself and they really didn't understand why. Now they know he was sick, they know why."

Looking back on all the years on the football field, she's angry that nothing was ever said about the dangers. The NFL has in recent years begun to take CTE seriously, amending its rules and bequeathing the Bedford VA brain bank $1m to fund its research. "We were never educated about brain injuries," Alicia says.

In Duerson's heyday, she recalls, if a player took a knock, the coach would hold up two fingers and say "how many can you count?", the player would say "three" and the coach would send them back on to the field.

"They treated it like a joke," Alicia says. "But that wasn't a joke."