People magazine broke the news today (29th June), with Holmes' attorney Jonathan Wolfe releasing a statement.
Wolfe said: "This is 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."
Cruise's representative Amanda Lunberg has since revealed that Tom is "deeply saddened", following Holmes' decision to file divorce paperwork in New York City.
Lunberg stated: "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."
TMZ has reported that the couple previously signed a prenuptial agreement in order to decide how to split their multi-million dollar fortune if they were to ever break up.
The US celebrity gossip website also claims that Katie hopes to gain full custody of their only child together, daughter Suri, aged 6.
Tom-Kat tied the knot back in November 2006 at an Italian castle, with Holmes giving birth to Suri earlier that year on 18th April.
Cruise - who is currently shooting new sci-fi flick Oblivion - recently gave no indication that his marriage with Holmes was in trouble during an interview with People last month, stating that their relationship was "very special."
The Rock Of Ages actor gushed: "She is an extraordinary person, and if you spent five minutes with her, you'd see it. Everything she does, she does with this beautiful creativity.
"She has a voice and warmth as an artist, as a mother. She's funny and charming, and when she walks into the room, I just feel better."
He added: "I'm a romantic. I like doing things like creating romantic dinners, and she enjoys that. I don't know what to say - I'm just happy, and I have been since the moment I met her. What we have is very special."