The Tampa Bay Devil Rays owned the number one pick and selected Hamilton with the first overall selection. Hamilton signed with Tampa Bay, receiving a $3. 96 million signing bonus, and joined their minor league system. His first stop in the minors was the rookie level Princeton Devil Rays of the Appalachian League, where he played 56 games. Hamilton later joined the Short Season Single-A club, the Hudson Valley Renegades, and helped lead them to their first New York–Penn League championship. He spent the 2000 season with the Charleston RiverDogs in the South Atlantic League. Hamilton enjoyed a breakout season during which he hit . 301 in 96 games, with 13 home runs and 61 RBIs. He was also selected to the South Atlantic League All Star game and took home MVP honors after going 2–6 with two triples and two runs scored. In addition, Hamilton was named to the 2000 All-Star Futures Game, a game designed to showcase minor league prospects. Hamilton was also voted Minor League Player of the Year by USA Today. At the start of his pro career, Hamilton's parents quit their jobs so they could travel with their son.