Miller was one of the best young pitchers in the National League (NL) before injuring the rotator cuff in his pitching shoulder in 2004.

In 2004, Miller was 7–7 with 74 strikeouts and a 3.35 ERA in 15 starts before going on the disabled list in June with a season-ending rotator cuff injury.

The Astros believed he was playing hurt with shoulder and elbow injuries much of the year before, but Miller never complained about them.

On November 9, 2006, Miller signed an incentive-laden, $1.5 million one-year extension to stay with the Cubs under new manager Lou Piniella.

In a nine-year MLB career, Miller compiled a 62–46 record with 749 strikeouts and a 4.10 ERA in 894+1⁄3 innings pitched.