"This is a personal and private matter for Katie and her family," lawyer Jonathan Wolfe told the celebrity news Web site. "Katie's primary concern remains, as it always has been, her daughter's best interest."
Cruise confirmed the news in a separate statement to People.com.
"Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children," his statement said. "Please allow them their privacy to work this out."
Neither party gave a reason for the split.
The couple married in November 2006 and are the parents of a 6-year-old daughter, Suri.
This was Holmes' first marriage.