The musical follows an unlikely tale of two Mormon missionaries who find more than they bargained for in Africa. It was written by Trey Parker and Matt Stone, who are the creators of Comedy Central's "South Park," and Robert Lopez, co-creator of the Tony Award-winning musical, "Avenue Q." All got nominations.
In "South Park," Parker and Stone have lampooned everything and everybody from Jesus to Saddam Hussein to Barbra Streisand to Scientology to Tiger Woods to New Jersey.
As for the Mormons, the church would not add to the comment they first issued when the musical opened: "The production may attempt to entertain audiences for an evening, but the Book of Mormon as a volume of scripture will change people's lives forever by bringing them closer to Christ."
"The Scottsboro Boys" received the second-highest number of nominations, including best musical, best book of a musical, best original score and leading actor and two feature actor nods.
"Mormon" and "Scottsboro" face competition from "Catch Me If You Can" and "Sister Act" for best musical. The plays that were nominated include the human-puppet hybrid "War Horse," David Lindsay-Abaire's "Good People," Jez Butterworth's "Jerusalem" and Stephen Adly Guirgis' "The Motherf---- With the Hat."
Among individual actors who earned nominations were Al Pacino, who played Shylock in "The Merchant of Venice," Vanessa Redgrave in "Driving Miss Daisy," Edie Falco in "The House of Blue Leaves" and Ellen Barkin in "The Normal Heart."
The awards will be handed out June 12 at the Beacon Theatre.
The Associated Press contributed to this report.