The Clockwork Orange, while being by far his most famous work, is despised by Burgess. He feels it is a mediocre work near the grungy bottom. It probably only became quite so popular because of Stanley Kubrick's excellent film. This is one of the few films that can be respectfully acknowledged by a reader of the book. Although Kubrick doesn't do the movie precisely following the book, he takes liberties only where necessary. Well, besides the last chapter anyway, which is entirely missing.

My source for the Burgess vs. Clockwork Orange hate is his own introduction to the 21-chapter American version of A Clockwork Orange, ISBN: 0-393-31283-6 from Norton & Company.
Here are some excerpts:

"I first published the novella A Clockwork Orange in 1962, which ought to be far enough in the past for it to be erased from the world's literary memory. It refuses to be erased, however, and for this the film version ... may be held chiefly responsible. I should myself be glad to disown it for various reason, but this is not permitted."

"A Clockwork Orange has never been published entire in America." ... "21 is the symbol of human maturity ... the number 21 was the number I started out with." ... "The number of chapters is never arbitrary" ... "Those twenty-one chapters were important to me."
"But they were not important to my New York publisher." ... "He insisted on cutting out the twenty-first."
"Now when Stanley Kubrick made his film--though he made it in England--he followed the American version..." .. "Audiences did not exactly clamour for their money back, but they wondered why Kubrick left out the denoument. People wrote to me about this--indeed much of my later life has been expended on Xeroxing statements of intention and the frustration of intention--while both Kubrick and my New York publisher coolly bask in the rewards of their misdemeanour. Life is, of course, terrible."

Then he talks to a great extent on the purpose of the 21st chapter, and how very terrible it was to have been taken out. This may have had a great deal of impact on his current distaste(up until death in 1993) of the book.

"We can destroy what we have written but we cannot unwrite it. I leave what I wrote with what Dr. Johnson called fridged indifference to the didgement of that .00000001 of the American population which cares about such things. Eat this sweetish segment or spit it out. You are free."
Anthony Burgess November, 1986