Khaled Hosseini has joined the illustrious ranks of Philip Pullman and the authors of a story about gay penguins, after his novel The Kite Runner became one of the books that inspired most complaints in America last year.

The bestselling and critically acclaimed title, the story of a 12-year-old Afghan and his betrayal of his best friend, includes the rape of a boy, and provoked challenges in the US over what objectors saw as sexual content and offensive language. Some objections led to the removal of the book from library shelves, while others saw it replaced with bowdlerised versions minus the offending scenes, according to the American Library Association, which compiles an annual list of the most challenged titles in the country.

Topping this list in 2008 was, for the third year running, Justin Richardson and Peter Parnell's And Tango Makes Three, a children's book about two male penguins who bring up an orphaned chick. Based on a newspaper story the authors saw about a zookeeper who noticed two of his penguins trying to hatch a stone, the book was criticised for being pro-gay, anti-religion and anti-family.

"Books that address same-sex parenting, or same-sex relationships, are particularly prone to challenges in the US," said Deborah Caldwell-Stone, deputy director of the ALA's office for intellectual freedom, which has collected information on challenged books for the last 20 years. "In the case of And Tango Makes Three, there are many parents who believe it inappropriate to teach children anything at all about homosexual relationships, even in the form of a picture book about a true story."

Another stalwart of the ALA's list, Philip Pullman's His Dark Materials trilogy, rose to second place overall in 2008 from fourth the previous year, distressing challengers over its political viewpoint, religious viewpoint and violent scenes. Last year Pullman said his immediate reaction on hearing the news was "glee". "They never learn," he said. "The inevitable result of trying to ban something – book, film, play, pop song, whatever – is that far more people want to get hold of it than would ever have done if it were left alone. Why don't the censors realise this?"

Caldwell-Stone said the film of The Golden Compass, based on the first novel in Pullman's trilogy, had renewed attacks on the sequence from Catholic pressure groups. "In many cases school boards reacted precipitously and removed it – then a few weeks later they returned it to the shelves," she said.

This year, challengers appeared to be focusing their efforts on more recent releases, with Mark Twain's The Adventures of Huckleberry Finn (which had drawn criticism for racism), Alice Walker's The Color Purple (challenged for sexual content, homosexual content and offensive language) and Maya Angelou's I Know Why the Caged Bird Sings (sexual content) all dropping out of the top 10 after riding high last year.

The ALA recorded 513 challenges in 2008, up from 420 in 2007. The ALA defines a challenge as "a formal, written complaint, filed with a library or school, requesting that materials be removed or restricted because of content or appropriateness". It estimates that as few as one in five challenges are actually reported. "We believe this is just the tip of the iceberg," said Caldwell-Stone.

Seventy-four books were actually removed from shelves following challenges last year, the ALA said, ranging from Jodi Picoult's bestselling novel My Sister's Keeper, pulled for its sexually explicit content, to Sherman Alexie's The Absolutely True Diary of a Part-Time Indian, which includes references to masturbation. Alexie's comments at the time echoed Pullman's, with the author telling local press that "the amazing thing is these banners never understand they are turning this book into a sacred treasure. We don't write to try and be banned, but it is widely known in the [young adult] world, we love this shit."

"While not every book is right for each reader, every reader has the right to choose reading materials for themselves and their families and should be able to find those materials in libraries, classrooms, and bookstores. Our goal is to protect one of our most precious fundamental rights - our freedom to read," said Caldwell-Stone.

The ALA celebrates all banned and challenged books every year with Banned Books Week, founded by Judith Krug, a tireless anti-censorship campaigner who died last week after a long illness, aged 69. Often quoted as saying that "censorship dies in the light of day", Krug was the director of the ALA's office for intellectual freedom and executive director of its Freedom to Read Foundation for more than 40 years.

"Judith had an abiding faith in the power of 'the community of the book' – she was convinced that when librarians, publishers, booksellers, and authors stand together in defence of intellectual freedom we are unstoppable. She believed in our obligation to take on that fight wherever and whenever it arose, and more often than not she led the charge," said Judith Platt, president of the Freedom to Read Foundation. "She considered librarianship to be the highest of callings and there is an entire generation of librarians out there whose commitment to intellectual freedom was forged and shaped by Judith Krug."

The ALA's top ten most frequently challenged books of 2008 in full:

1. And Tango Makes Three by Justin Richardson and Peter Parnell

Reasons: anti-ethnic, anti-family, homosexuality, religious viewpoint, unsuited to age group

2. His Dark Materials trilogy by Philip Pullman

Reasons: political viewpoint, religious viewpoint, violence

3. TTYL; TTFN; L8R, G8R series by Lauren Myracle

Reasons: offensive language, sexually explicit, unsuited to age group

4. Scary Stories series by Alvin Schwartz

Reasons: occult/satanism, religious viewpoint, violence

5. Bless Me, Ultima by Rudolfo Anaya

Reasons: occult/satanism, offensive language, religious viewpoint, sexually explicit, violence

6. The Perks of Being a Wallflower by Stephen Chbosky

Reasons: drugs, homosexuality, nudity, offensive language, sexually explicit, suicide, unsuited to age group

7. Gossip Girl series by Cecily von Ziegesar

Reasons: offensive language, sexually explicit, unsuited to age group

8. Uncle Bobby's Wedding by Sarah S. Brannen

Reasons: homosexuality, unsuited to age group

9. The Kite Runner by Khaled Hosseini

Reasons: offensive language, sexually explicit, unsuited to age group

10. Flashcards of My Life by Charise Mericle Harper

Reasons: sexually explicit, unsuited to age group