Downs was a fifth-round draft choice of the Chicago Cubs in June 2003. As a member of the Arizona League Cubs, Downs appeared in a total of 13 games during the 2003 minor league season, making 11 starts. He posted an earned run average (ERA) of 6.57 and had an 0–2 record.\n', '

For the 2004 season, Downs played for another Cubs minor league affiliate, the Boise Hawks. He pitched in 14 games, all but one as a starter. His ERA (4.95) was better than that of the previous year, as was his record of 5–3. Also, he struck out 61 opponents, the most by any Boise pitcher that season.\n', '

Downs remained with Boise for most of 2005 and for the second consecutive season, he appeared in 14 games for the team and started 13 of them. With Boise, his ERA dropped again, this time to 3.50, and his win–loss record was 5–4. During his time with the Hawks, Downs also struck out 63 opponents. However, he actually began the year with the Peoria Chiefs, where he started and lost two games, posting a bloated ERA of 18.47.\n', '

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