"This is a personal and private matter for Katie and her family," said Katie's lawyer in a statement. "Katie's primary concern remains, as it always has been, her daughter's best interest."
Tom's rep told People magazine that "Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children. Please allow them their privacy."
Tom, 49, and Katie, 33, were married in 2006 among much couch-jumping fanfare.
TMZ say the pair had been wearing their wedding rings all week, and Tom was "blindsided" by Katie's demand for "primary residential custody" of their six-year-old daughter.
The couple were rumoured to have a prenuptial agreement that gave Katie $3 million for every year of the marriage, and a big mansion in California if the couple split.
TomKat fans and haters alike don't seem shocked by the news, with many tweets running along the lines of this one by user @alex_rulz: "Katie Holmes' five-year, $325-million dollar contract has not been renewed. Tom Cruise now on the search for a beard replacement."