L.A. Superior Court spokesperson Pat Kelly tells PEOPLE, "Yes, it's confirmed. It was filed today, on the grounds of irreconcilable differences." TMZ.com was the first to report the filing.
Spears and Federline wed in September 2004 and have two sons, Sean Preston, 1, and Jayden James, who was born Sept. 12.
According legal documents filed on Tuesday in Los Angeles, Spears seeks custody of both boys, with Federline getting visitation rights.
Spears gives a separation date of Monday. She asks that each party pay their own legal fees and waives her right to spousal support. She also requests that certain assets, including "miscellaneous jewelry and other personal effects," be confirmed as separate property.
She and Federline, 28, both spent the weekend in New York City, but Spears did not appear at any of the events promoting Federline's new CD, Playing with Fire.
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But the previous week, he admitted that, because of his touring schedule, "I'm not going to see my family as much as I want to, but I mean, those are the sacrifices you make as an artist."