The office of celebrity divorce lawyer Jonathan Wolfe confirmed the divorce. "This is a personal and private matter," he said in a statement.
They have a six-year-old daughter, Suri, and Cruise, 49, has two children from his marriage to Nicole Kidman.
Cruise married Holmes, 33, his third wife, in an Italian castle in November 2006.
A spokesman for Cruise told the BBC: "Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children. Please allow them their privacy."
TMZ News has reported that Holmes filed divorce papers in New York on Thursday, citing irreconcilable differences, and that she is seeking sole custody of their daughter.
'Something happened'
The divorce brings to an end a relationship that began with very public declarations of affection.
Continue reading the main story
Analysis
Jeanne Wolf
Hollywood entertainment reporter, Los Angeles
In Hollywood, people's mouths are hanging open. Apparently even Cruise did not see this coming. We know that Holmes tried to file for divorce anonymously but somehow her name got out. Cruise and Holmes were a popular couple but tended to keep to themselves.
But they have talked a lot about each other - about how much they loved each other - and although we do not know details about pre-nuptial agreements, we can be sure that if there are any, they have as much to do with secrecy as with money.
What we can expect next is a lot of wild speculation, especially over Holmes' request for sole custody of their daughter - people may wonder if Cruise's belief in Scientology was a factor in her decision.
Holmes once admitted she had a childhood crush on the Hollywood celebrity, while Cruise famously jumped on a sofa on the Oprah Winfrey Show as he declared his love for Holmes.
"I can't be cool. I can't be laid-back. Something happened and I want to celebrate it," Cruise said in his appearance on the show.
Cruise proposed to Holmes at the Eiffel Tower in Paris and the couple were married by a Church of Scientology minister.
The couple, who have not been seen together since February, are estimated to be worth about $275m (£175m) combined.
Tom Cruise is among Hollywood's highest-paid actors and has starred in blockbusters such as Top Gun, Jerry Maguire and the Mission Impossible series.
Earlier this week he was reported to be in Iceland shooting an upcoming film called Oblivion. He also starred in the recently released Rock Of Ages.
Katie Holmes rose to fame as a leading actress on US television drama Dawson's Creek. She has also appeared in Batman Begins and Don't Be Afraid Of The Dark.
http://marquee.blogs.cnn.com/2012/06/29/report-tom-cruise-katie-holmes-set-to-divorce/
http://www.bbc.co.uk/news/entertainment-arts-18653268
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Gonna take some time to do the things we never had
