Patterson was selected by the Chicago Cubs as the third overall pick in the 1998 Major League Baseball draft. He made his professional debut in 1999 with the Lansing Lugnuts of the Class-A Midwest League, and was selected as that league's "Prospect of the Year" after leading the league in slugging percentage (.592), extra base hits (72) and triples (17). He also batted .320 with 20 homers and 79 RBI, and was named to the league's all-star team both at mid-season and postseason. "Baseball America" named Patterson the league's top prospect. After the 1999 season, he played in the Arizona Fall League and was that league's youngest player. He batted .368 with 4 home runs, 24 RBI, and 8 stolen bases in 35 games, and was named to the league's all-star team.