With Class-A Rome in 2004, Reyes struggled most of the season, going 2-5 with a 5.33 ERA. Tommy John surgery kept him out for the end of the year and the first half of the 2005 season. He was sent back to the GCL in 2005, and after doing well received a mid-season promotion to Class-A Danville. While his strikeout total fell (27 in 43 innings), he went 3-0 with a 3.53 ERA and posted a WHIP of 0.99, but a torn anterior cruciate ligament (ACL) ended his season prematurely.