The 10-year-old Irish-bred horse collapsed after narrowly beating Thistlecrack to win the Cotswold Chase at Cheltenham's Festival Trials Day.
He was treated by veterinary staff before being pronounced dead.
The British Horseracing Authority confirmed the horse suffered from a "severe pulmonary haemorrhage".
Tony Welsh, acting chief veterinary officer for the BHA, said: "Episodes such as this are rare, and can occur in horses which have no underlying health issues, and amongst all disciplines of sport horses.
"In spite of the rarity of these incidents, as a sport we are determined to do more to understand what causes these symptoms, and whether more can be done to prevent it."
In Saturday's race, King George winner Thistlecrack caught Many Clouds close to the finish but the Trevor Hemmings-owned gelding, ridden by Leighton Aspell, fought back to win.
Many Clouds had shown symptoms of post-race ataxia in the past, which had seen him over-heat and "wobble" on his feet, but the horse had never collapsed before, and had shown no symptoms of post-race ataxia on Saturday.
Many Clouds had previously won the Gold Cup trial in 2015 and the Hennessy Gold Cup in 2014.
Trainer Oliver Sherwood described him as the "horse of a lifetime".
BBC horse racing correspondent Cornelius Lysaght
The crucial words here are "no significant underlying health issues".
On more than one occasion, notably after his Grand National success, Many Clouds received treatment for a tendency to 'overheat', but he soon recovered, and his welfare was closely monitored by the authorities as a result.
With that fact in mind, questions have been raised as to whether that condition was linked to his death, but this report concludes he was the victim of a haemorrhage rarely seen on the racetrack.

Guiseley managed to frustrate Dover during a first half that was dominated by the hosts, but Dover kept plugging away and took complete control just after the break.
Ricky Miller underlined his position as the National League's top marksman by slotting his 19th of the season after 46 minutes, beating two defenders before firing hard and low past Jonathan Maxted.
Moses Emmanuel profited from slack defending three minutes later to make it comfortable for the hosts, who remain sixth and one point off the play-off places.
Report supplied by Press Association.
Match ends, Dover Athletic 2, Guiseley 0.
Second Half ends, Dover Athletic 2, Guiseley 0.
Substitution, Dover Athletic. Aswad Thomas replaces Sam Magri.
Substitution, Guiseley. Michael Rankine replaces Adam Boyes.
Substitution, Guiseley. Joel Logan replaces Jordan Preston.
Goal!  Dover Athletic 2, Guiseley 0. Moses Emmanuel (Dover Athletic).
Goal!  Dover Athletic 1, Guiseley 0. Ricky Miller (Dover Athletic).
Second Half begins Dover Athletic 0, Guiseley 0.
First Half ends, Dover Athletic 0, Guiseley 0.
Ashley Palmer (Guiseley) is shown the yellow card.
Connor Brown (Guiseley) is shown the yellow card.
Moses Emmanuel (Dover Athletic) is shown the yellow card.
Ricky Miller (Dover Athletic) is shown the yellow card.
Danny East (Guiseley) is shown the yellow card.
First Half begins.
Lineups are announced and players are warming up.

Comley, 20, has played twice for the R's first-team and signed a two-year deal at Loftus Road in May, having been with the club since the age of nine.
His full debut came as a substitute in last season's 5-1 Premier League defeat by Leicester City.
"We like what we've seen from Brandon and we think we can work with him," Carlisle boss Keith Curle said.
The Islington-born midfielder, who featured in a trial match for Carlisle against Barrow, will return to his parent club on 20 February.
A post mortem examination revealed Many Clouds died from bleeding on the lung but that the 2015 Grand National winner had no underlying health problems.
[NEXT_CONCEPT]
Dover kept up the pressure on those on in the National League playoff places with a comfortable 2-0 win over strugglers Guiseley at the Crabble Athletic Ground.
[NEXT_CONCEPT]
Carlisle United have signed midfielder Brandon Comley from from Queens Park Rangers on a one-month youth loan.