Holmes's attorney Jonathan Wolfe confirmed the news with a statement earlier today (June 29), reports People.
"This is a personal and private matter for Katie and her family," Wolfe said. "Katie's primary concern remains, as it always has been, her daughter's best interest."
Cruise's representative Amanda Lunberg revealed that her client is "deeply saddened", following Holmes filing the paperwork in New York City.
"Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children," Lunberg commented. "Please allow them their privacy to work this out."
Holmes intends to gain full custody of their 6-year-old daughter Suri, according to TMZ.
The website also reports that the pair have a prenuptial agreement over their multi-million dollar fortune.
> Tom Cruise, Katie Holmes to divorce - Relationship in pictures
Cruise also has two children from his previous marriage to Nicole Kidman, with whom he broke up in 2001.
The Top Gun actor has been married three times, first with Mimi Rogers between 1987 and 1990.
Holmes's marriage to Cruise at an Italian castle in November 2006 was her first.
Cruise is presently shooting movie Oblivion, while Holmes remains in New York City with daughter Suri.
Speaking earlier this month, the 49-year-old declared his intention not to have any more children with his 33-year-old wife.
Photo gallery - Tom Cruise and Katie Holmes's relationship through the years:
Copyright: Rex FeaturesWatch Tom Cruise discuss Mission: Impossible - Ghost Protocol with Digital Spy below: