The latest school to excise the book is National Cathedral School in Washington, an elite private academy for girls attended by Vice President Al Gore's daughters.
Once upon a time the controversial tale of a 14-year-old boy and his friend, Jim, a runaway slave, was required reading at the National Cathedral and its brother school, St Alban's. Both have decided to take a new look at the book and to reintroduce it as an option for 11th and 12th graders (sixth-formers).
Published in 1885 and couched in a dialect that has vanished, Huckleberry Finn engenders concern because of its portrayal of black people and the use of the "n" word, "nigger". The word appears in the first line and more than 200 times thereafter - it was, after all, the word used to describe a black person in the last century.
Ernest Hemingway claimed the novel is where "all modern American literature comes from" and many state schools in the Washington suburbs do teach it - despite the worries that have existed for decades.
However, not all pupils at the two elite Washington schools are happy with today's political correctness, and some are accusing their teachers of oversensitivity and not crediting them with the intelligence to see that the book was a product of its time.
"As an African American male, you must understand why the book was written and how it was written," said a black 17-year-old at St Alban's. "We are smart enough to understand that."
Those who defend the book point to Twain's portrayal of an inter-racial relationship in a society that was deeply divided by race and the way the white boy learnt to see beyond the colour of Jim's skin.
They say that Jim is the most attractive character in the book, and that Huckleberry Finn must be seen in its context and should be taught to help American children understand their history. However, those who disagree believe that the book is too difficult for younger pupils - hence the two private schools' intention to teach it to older children.
At Sidwell Friends School, the private Quaker institution attended by the President's daughter, Chelsea Clinton, 11th graders studied the book last year. And it remains on Sidwell's suggested reading list for younger pupils.
But the book is definitely not taught at Mark Twain Intermediate School in Fairfax county, northern Virginia, where there was a national campaign during the 1980s to drop it.
According to the latest survey from People for the American Way, the civil liberties group, the story was the fifth most controversial book between 1982 and 1994.
Even more controversial, for example, were Of Mice and Men by John Steinbeck, and Catcher in the Rye by JD Salinger.
Meanwhile at National Cathedral School this year's 15-year-olds are no longer struggling with Huck's dialect. Instead they are reading F Scott Fitzgerald's The Great Gatsby and Henry James's Daisy Miller. One reason was that Twain's tale required a better knowledge of history than most American children have.