He's asking for $50 million in damages from the magazines' parent company, Bauer Publishing.
Cruise filed the defamation lawsuit Wednesday in Los Angeles over cover stories that suggested he'd "abandoned" his 6-year-old daughter, Suri.
Cruise's attorney, Bert Fields, says the actor is a caring father, and Suri is a "vital part of his life."
Fields released a statement saying "To say he has 'abandoned' her is a vicious lie. To say it in lurid headlines with a tearful picture of Suri is reprehensible."
Fields added that Cruise doesn't like to file lawsuits but felt it was appropriate because "sleaze peddlers" are trying to make money about the actor's relationship with his daughter.
If Cruise prevails, Fields said his client would give the money to charity.
Cruise and Suri's mother, Katie Holmes, divorced earlier this year after six years of marriage. The breakup has been tabloid fodder, and Suri often appears in entertainment magazines.
The Associated Press contributed to this report.