I think Joe Frazier, Michael Spinks, and Larry Holmes, he had a couple of other losses too but I don't know against who. Joe Frazier is the most significant one, because when Frazier fought him, Ali was still relatively deadly as a fighter. If the Ali who fought Lison the first time was 100%, the one who fought Frazier, was 85%, BUT, Ali's ringcraft due to his experience, was 120%, whereas the inexperienced Cassius Clay who faced Liston was all reflexes, no "old warrior" cunning at all. To Frazier's credit, a worldwide ancient proverb is in order here;
From ancient to midieval times, all over the world, there was this proverb, a warning given to all young men who ever took up the sword;
"Beware of an old warrior my son; what they lack in youth, they more than make up for with the cunning of experience, and tricks they've picked up."
Indeed within Viking society for example, many 18 year old youths lost their lives against men in their 50's. True enough most boxers start losing their edge as they get older, but you have to remember that in boxing, damage accumulates with the years, and the body rapidly begins to lose many of its functions. Boxers generally age much faster, because between the brutal physical work, and the constant battering, its a vicious cycle of train, get beat up, train some more, take another beating, and even if a boxer wins, he loses, all those blows to the body and head take their toll.
With ancient and midieval warfare, you were dealing with bladed weaponry, and sharpened spears, if a man lived to be 50, that in and of itself was a feat, hence the reason why another version of the proverb goes;
"while young wolves may be ferocious, its the old ones, who are the most dangerous."
In fact in Spartan society, all military service ended at the age of 60; it was recognized by the ancient Spartans, that a physically fit man held on to much of his strength well into his 50's. Not all of it, but enough to cause you problems if its a "there is nothing you can do, that I haven't already seen" situation.
Again to Joe Frazier's credit, he knocked out somebody with more ring experience and cunning than him.
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He lost five times in his pro career, finishing with a career record of 61-56(37)-5.
The people who beat him were:
Joe Frazier (unanimous decision August 1971)
Ken Norton (split decision March 1973)
Leon Spinks (split decision February 1978)
Larry Holmes (TKO October 1980)
Trevor Berbick (unanimous decision December 1981)
Those last three came well after the peak of his career and came in the space of his last four fights - like so many fighters, he went on for far too long. He retired after losing to Berbick.
He lost to LeonSpinks and Joe Frasier but regained his title soon after.
Ali Loses:
source: http://en.wikipedia.org/wiki/Muhammad_Ali