A spokeswoman for Harper Collins in New York said Lee passed away peacefully yesterday. The Pulitzer-winning author shunned the spotlight for decades and spent her final years living in seclusion in Monroeville, Alabama, where she was born.
"To Kill a Mockingbird" is considered one of the great classics of 20th century American literature, and is standard reading in classrooms across the world.
Published in 1960 and drawn from Lee's own experiences as a child, it came to define racial injustice in the Depression-era South.
The novel sold 30 million copies and won huge critical acclaim, thrusting Lee into the limelight, winning her the Pulitzer in 1961 and an avalanche of publicity.
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Her fame was sealed when the novel was adapted into a Hollywood film that won three Academy Awards in 1963, including an Oscar for Gregory Peck for his portrayal of Finch, one of the best-loved characters in American fiction.
"The world knows Harper Lee was a brilliant writer but what many don't know is that she was an extraordinary woman of great joyfulness, humility and kindness," said Harper Collins president Michael Morrison.
In a rare insight, the novelist admitted in 1964 she had been completely caught off guard by being catapulted into the nation's consciousness by her novel.
"I hoped for a little, but I got rather a whole lot and in some ways this was just about as frightening as the quick, merciful death I'd expected," she said, joking about her expectation the novel would be a critical flop.
For decades she stayed out of the public eye, claiming to have said all she wanted in "Mockingbird" and vowing never to publish another book.
The manuscript was an instant popular bestseller but it was mauled by critics, and its release sparked torrid speculation that the author, who suffered a stroke in 2007, was not of sound mind.
Born Nelle Harper Lee in April 1926, she was the youngest of four children. Her father was a lawyer and a direct descendant of Civil War general Robert E. Lee.
Lee grew up during the Great Depression in a remote village where the few available books provided the only entertainment. She never married, and books remained forever her first love.