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Critics, usually parents, regularly accuse JK Rowling's tales of a trainee sorcerer of "Satanism".
John Steinbeck's classic Of Mice and Men and Maya Angelou's I Know Why The Caged Bird Sings are also on a list of "challenged" books.
The American Library Association (ALA) publish the list to highlight the fact that many books widely considered to be classics are often criticised in this way.
Judith Krug of the ALA says it issues the list "to raise awareness about censorship and remind Americans that our freedoms can be fragile if we are not vigilant in protecting them".
The ALA defines a challenge as a formal, written complaint filed with a school library about a book's content or appropriateness.
Nobel Winner Steinbeck's Of Mice and Men was criticised for its strong language and violence.
The book tells the story of a pair of lonely drifters living on the margins of society in California.
It was made into a 1992 film starring John Malkovich and Gary Sinise.
Poet Angelou, who recited her work at the inauguration of former US President Bill Clinton, published I Know Why The Caged Bird Sings in 1970.
The first volume of her autobiography later became a best-seller in the US.
It has been challenged on the grounds that it includes racism and sexual content.
Other books on the list include Robert Cormier's The Chocolate War, cited for violence and Caroline Cooney's The Terrorist.
The Terrorist is a young adult novel about a boy killed after being handed an explosive package on a London train.
The book proved controversial long before the recent attacks on the US.
"The complaints are because the alleged terrorist is an Arab," Krug said.
The ALA reports 646 challenges in 2000, up from 472 in 1999, and believes this represents just a fraction of actual complaints.
But Krug added that books rarely end up being banned.