Holmes filed papers in New York City on Thursday, citing irreconcilable differences and seeking sole custody of the couple's six-year-old daughter Suri in a move that came "out of the blue" for the Mission: Impossible actor, said one source with knowledge of the situation.
The source said Cruise is out of the country filming a movie in Iceland and the filing came as a surprise.
The actor's spokeswoman issued a brief statement, saying, "Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children. Please allow them their privacy to work this out." No further comment was made.
Los Angeles-based attorney Bert Fields, who has represented Cruise in other matters but is not handling the divorce, confirmed the filing but declined to give further details.
"Tom wants to be very private," Fields said.
Earlier on Friday, People magazine quoted Holmes' attorney Jonathan Wolfe as calling it "a personal and private matter for Katie and her family ... Katie's primary concern remains, as it always has been, her daughter's best interest."
The couple's marriage, which began at an elaborate, Italian castle wedding in November 2006, has been closely followed by the celebrity press ever since the pair, dubbed TomKat, began dating in 2005.
At the time, Holmes, now 33, was a rising star and Hollywood ingénue who found fame on TV's Dawson's Creek and earned her acting chops in independent films such as Pieces of April.
Cruise, 16 years her senior, was among Hollywood's highest paid stars who enjoyed a string of box office blockbusters in action flicks ranging from 1986's Top Gun to his Mission: Impossible movies that began in 1996 and continue today.
He proposed to Holmes atop the Eiffel Tower in Paris and famously went on Oprah Winfrey's talk show, jumped on her couch and shouted out his love for Holmes in front of a TV audience of millions.
Cruise, a practitioner of Scientology, was previously married to actress Mimi Rogers and actress Nicole Kidman, with whom he has two children.
Holmes' marriage to Cruise was her first.
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@harkol: Katie Holmes filed for divorce, not Tom Cruise. She didn't want Suri to grow up following Scientology apparently.
@harkol: In some peoples' opinion, he simply changes his beard. Unlike John Travolta.
Whtever the case maybe .. i am a huge Fan of Tom and wish him all the best.....though i sincerely hope it works out well for these two..
Sad end of a fairy-tale :(
Tom Cruise divorces his wifes when their age reaches 33-34 and moves on to a younger woman. He is consistent in doing it.
If any of these women expected any different - they are fools.