The novelist and children's writer Philip Pullman has been showered with awards that include a CBE, a Carnegie Medal and several honorary professorships. This week he notched up a new distinction: he is ranked second in the top 10 books that people have tried to ban across America.

Pullman's fantasy trilogy, His Dark Materials, has leapt to the top of the target list of would-be censors in the new rankings issued this week by the American Library Association. It tracks cases where individuals or groups have attempted to have books stripped from bookshelves in schools and libraries across the US.

Its newly released rankings for 2008 recorded 513 cases where books were targeted for censorship, of which 74 were successfully banned or restricted. Pullman's trilogy was the second most commonly attacked, a result, the ALA believes, of an organised campaign that the anti-defamation group the Catholic League launched against the film version of The Golden Compass.

Several schools across America faced requests from parents to remove the book. One challenge at a school in Winchester, Kentucky was made on the grounds that the book's main character drinks wine and eats poppy with her meals. Another school in Oshkosh, Wisconsin pulled the trilogy because of its "anti-Christian message".

Reached by the Guardian, Pullman quipped that he was "very glad to be back in the top 10 banned books". But he added: "Of course it's a worry when anybody takes it upon themselves to dictate what people should or should not read. The power of organised religion is very strong in the US, and getting stronger because of the internet."

Almost 4,000 attempts to ban books have been recorded over the past eight years, though the ALA believes the figure is a gross understatement. All cases are voluntarily reported, and many more are likely to go unrecorded, sometimes because librarians have been threatened with dismissal if they sound the alarm. Most would-be censors are parents concerned about their children's reading or members of religious groups. The most common complaint is against books with explicit sexual content or offensive language.

In recent years, the ALA has spotted a growing intolerance towards children's books that deal with homosexuality - a quality most famously displayed by Sarah Palin who tried in the late 1990s as then mayor of Wasilla in Alaska to have Daddy's Roommate, a tale about a gay father, removed from the town library.

Three of the top 10 most challenged books in 2008 had gay or lesbian characters, including the single most censored volume, And Tango Makes Three. The fact that it tells the true story of two gay penguins at the Central Park zoo in New York does not appear to have placated opponents.

Nor does the fact that number eight on the list, Uncle Bobby's Wedding, features a couple of gay guinea pigs. Deborah Caldwell-Stone, acting director of the ALA's office for intellectual freedom that compiles the censorship list, says that children of gay and lesbian couples have found such books valuable. "Kids with same-sex parents are thrilled to find books in school libraries that reflect their lives.

"That's why it's so important to resist censorship. We believe parents do have the right to dictate their children's reading, but that right exists for their children alone and should not be extended to others."

As Pullman's high ranking shows, religion is another major cause of complaints, and within that an important subset are books featuring witchcraft. The subject was put in relief this week when Matt Latimer, a former speechwriter for George Bush, alleged in his new memoir of life in the White House that Bush had refused to grant JK Rowling the Presidential Medal of Freedom because her writing "encouraged witchcraft".

The Harry Potter books have been a mainstay of the ALA's banned list since the late 1990s; in Georgia a Christian missionary is still waging a one-woman battle to have them removed from all state schools.

In the 2008 top 10, two separate volumes were objected to on groups of witchcraft or satanism - Scary Stories and Bless Me, Ultima. In many cases, the censorship bids are lodged by fundamentalist Christian groups that take the Bible's admonition to fight witchcraft literally.

Some of the most cherished books in the American literary cannon have fallen foul of censorship rows by dint of their language or sexual content.

Titles that have made it to the ALA's banned list in recent years include JD Salinger's The Catcher in the Rye (it includes many "fucks"); John Steinbeck's Of Mice and Men (for its strong language and political message that riles conservatives); and The Colour Purple by Alice Walker (people have objected to its homosexual theme and offensive language). The left is as capable of censoring as the right. A regular entry is The Adventures of Huckleberry Finn which anti-racists have tried to ban on grounds that Mark Twain uses the word "nigger".

As for Pullman, he confidently expects to be back in the top 10 next year.

His forthcoming book, a novel for adults, is called The Good Man Jesus and the Scoundrel Christ.