Katie is believed to have filed divorce papers anonymously in New York citing "irreconcilable differences." Tom is believed to have "not seen" the divorce documents coming.
Tom - who has been married twice before to Nicole Kidman and Mimi Rogers - wed the former 'Dawson's Creek' actress in an Italian castle in November 2006.
He is believed to currently be in Iceland filming new movie 'Oblivion' while Katie is in New York.
Tom recently gushed about his wife saying he loved her "creativity" and claiming their relationship was "very special".
He said: "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.
"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."
Katie reportedly wants sole legal custody of their six-year-old daughter Suri. The actress has asked for legal custody, primary residential custody and a "suitable amount" of child support from her husband, TMZ.com reports. In addition she has asked for the division of their property, although no mention of their pre-nuptial agreement is mentioned in the documents.
49-year-old Tom has confirmed he is upset about the demise of his five year marriage but is focusing on his children Connor, 17 and Isabella, 19 from his relationship with Nicole Kidman and his six-year-old daughter Suri. His representative said in a statement: "Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children. Please allow them their privacy."
Meanwhile, insiders close to the situation claim former 'Dawson's Creek' star Katie wanted to split from Tom - who has been married twice before - because she wants to "amp up her career".
A source told RadarOnline.com: "Katie just wants to live out of the spotlight of Tom. She wants to focus on her acting career, which has taken a backseat since her marriage.
"She is currently filming a movie and has another project lined up and she wants to amp up her career another notch, which she has struggled to do the past few years."
However, parenting style to their daughter Suri was also thought to be a problem.
The insider added: "Katie and Tom also have very different parenting views. Katie wants Suri to go to school with other children and have a grounded routine whereas Tom doesn't, he wants her schooled in the same manner as Connor andIsabella were. "Tom is nowhere near as strict as Katie is and doesn't believe in disciplining Suri, whereas Katie believes that is important. Tom basically treats Suri as a little adult, however Katie treats her like a six-year-old child, and that causes some major clashes over parenting style."
Tom recently said he did not want to have any more children because he was happy with his lot.
He said: "I'm so happy with three. I'm enjoying every second with Suri that I have. And I'm enjoying the relationship with my older kids, and the way it is right now."