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| 2007 |
2006 |
2005 |
2004 |
2003 |
| Pick # | Drafted By | Player | Dropped Player(s) |
| 1 | MIN | Mike Gonzales | - |
| 2 | SD | S. Torres | BJ Kim |
| 3 | TEX | Rodrigo Lopez | - |
| 4 | MIN* | Rowand | Stairs |
| 5 | CHI | Bonderman | E. Young, Glanville, Heredia |
| 6 | CLE | John Thomson | Baez |
| 7 | LA | Arroyo | Leskanic |
| 8 | STL | C. Silva | Worrell, Aurilia |
| 9 | OAK | JT Snow | G. Myers |
| 10 | LA* | Mench | R. Hammock |
| 11 | NY* | J. Buck | - |
| 12 | SD | C. Hammond | S. Burnett |
| 13 | TEX | D. Bush | Ligtenberg |
| 14 | OAK* | M. Alou | Villarreal |
| 15 | CHI | J. Niemann | Fuentes |
| 16 | CLE | Infante | Trachsel |
| 17 | LA | Madritsch | Koplove |
| 18 | STL | C. Izturis | R. Franklin |
| 19 | LA* | M. Holliday | J. Hairston |
| 20 | BOS | Jeremy Reed | Hasagawa, Borowski |
| 21 | STL | J. Tavarez | - |
| 22 | SD | T. Hollandsworth | R. Palmiero |
| 23 | LA | G. Rusch | Lohse |
| 24 | CLE | Wily Mo Pena | - |
| 25 | TEX | Jeff Francis | Batista |
| 26 | MIN | Menechino | Salmon |
| 27 | NY | C. Monroe | Moeller |
| 28 | CHI | D. Haren | Shuey |
| 29 | OAK | Alfonseca | Valverde |
| 30 | BOS | G. Carrara | Weber |
| 31 | STL | C. Blake | - |
| 32 | BOS* | Trever Miller | Matheny |
| 33 | NY* | Joel Guzman | Weathers |
| 34 | CLE | Adam LaRoche | A. Gonzalez |
| 35 | TEX | Mahay | - |
| 36 | MIN | O. Hernandez | Redman |
| 37 | NY | Stanton | Herges |
| 38 | CHI | JD Closser | A. Sanchez |
| 39 | OAK | Duchsherer | W. Alvarez |
| 40 | OAK* | Calero | Quantrill |
| 41 | STL | JC Romero | Frasor, Urbina, Gerut |
| 42 | OAK* | Quinlan | Moyer |
| 43 | NY* | Broussard | A. Cintron |
| 44 | CLE | Sizemore | Kennedy |
| 45 | TEX | Chase Utley | T. Adams, Greg Miller |
| 46 | MIN | G. Atkins | Borchard |
| 47 | NY | Maroth | T. Lee |
| 48 | CHI | A. Everett | T. Clark |
| 49 | OAK | Peralta | Wakefield |
| 50 | OAK* | Blanton | Soriano |
* indicates traded draft pick