Harris enjoyed an excellent start to the season, leading the league with five sacks after four games. He was instrumental in a Week 3 victory over the Vikings, disrupting a handoff in the Vikings backfield and forcing a fumble, which allowed the Bears to score the game-winning touchdown. Furthermore, Harris was awarded the NFC's "Player of the Week" award twice in three weeks. However, in the following weeks, Harris' productivity declined. Additionally, Harris was forced to leave the Bears' Week 13 match-up against the Vikings after sustaining a knee injury. Further medical review determined that Harris had severely injured his hamstring, and he missed the remainder of the 2006 season.