In 2000, Morris was selected in the first round (28th overall) of the NFL Draft by the Indianapolis Colts, where he spent his entire career. Morris started at middle linebacker for the Colts for the first 5 years of his career, and was the Colts' leading special teamstackler in the 2006 season. Morris also started 9 games for the Colts during the 2006 season, including 3 games in the playoffs and Super Bowl XLI, replacing Gilbert Gardner to improve the Colts' run defense. In 2001, Morris had his best statistical year with 114 total tackles (84 solo) and one sack. Morris was an unrestricted free agent after the 2006 season concluded and was re-signed by Indianapolis on March 5. He injured his left knee in the fourth game of 2007, and had season-ending surgery. He was released after a failed physical on February 27, 2008.