"I enjoyed my time in New England but feel this is the right time to pursue other opportunities," Pees said Thursday in a statement issued by the Patriots. "I had the privilege of working with some great coaches and great players over the past six seasons and leave the Patriots with some wonderful memories that will last a lifetime. In addition to the players and coaching staff, I want to thank the Kraft family, the media and the fans for all of their support."
Pees gave no further details about his decision and didn't mention his health.
Pees, 60, left the Patriots' Jan. 3 regular-season finale at Houston during the second half after suffering shortness of breath. He was hospitalized and flew back to New England the next day.
The Patriots allowed fewer than 20 points per regular-season game in each of Pees' four years as defensive coordinator. They gave up 17.8 this season, but they lost big fourth-quarter leads twice -- losing to the Indianapolis Colts 35-34 after leading 31-14, and to the Texans 34-27 after being ahead 27-13.
New England also allowed Baltimore's Ray Rice to score on an 83-yard run on the first offensive play of the playoff game and trailed 24-0 after the first quarter.
Pees joined the Patriots as linebackers coach in 2004 after he spent six seasons as head coach at Kent State. He took over as coordinator in 2006 after Eric Mangini left to become head coach of the New York Jets. Before going to Kent State, Pees was defensive coordinator and inside linebackers coach at Michigan State under Nick Saban, a close friend of Belichick.
The Patriots gave up the fifth-fewest points in the NFL this season (285). In Pees' first season as defensive coordinator, they allowed 237 points.
This likely will not be the only change to New England's coaching staff, according to NFL Network's Jason La Canfora. Belichick isn't pleased with how this season ended, La Canfora reported Thursday, and also could make a change on offense.
Traditionally, Belichick promotes from within, but Al Groh is a name to watch for the defensive coordinator vacancy, according to La Canfora. Groh has strong ties to Belichick and was fired as the University of Virginia's coach in November.
Groh also is a disciple of Bill Parcells and interviewed Wednesday for the Miami Dolphins' defensive coordinator job, which many around the NFL believe will be his for the taking. Therefore, it's conceivable that two of Groh's closest coaching mentors could end up in a bidding war for his services.
In-house candidates to replace Pees are Patriots defensive line coach Pepper Johnson and linebackers coach Matt Patricia.
The Associated Press contributed to this report.