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| 2007 |
2006 |
2005 |
2004 |
2003 |
| Pick # | Drafted By | Player | Dropped Player(s) |
| 1 | MIN* | Carl Pavano | Wendall |
| 2 | LA | Lyle Overbay | Ramon Ortiz |
| 3 | NY | Oliver Perez | F. Vina |
| 4 | MIN | Jack Wilson | Kielty |
| 5 | SD* | Sean Burnett | |
| 6 | CLE* | Daniel Cabrera | Dustin McGowan |
| 7 | STL | Westbrook | J. Phelps |
| 8 | CLE | Dallas McPherson | Ventura |
| 9 | TEX | Lidge | Cressend |
| 10 | SD | Kolb | Crudale |
| 11 | MIN* | Jason Bay | Burks |
| 12 | LA | Suppan | Affeldt |
| 13 | NY | Johnny Estrada | Jose Acevedo |
| 14 | MIN | Craig Wilson | Rhodes |
| 15 | CHI | Merker | Scott Stewart |
| 16 | BOS | V. Castilla | Ben Davis |
| 17 | STL | Doug Davis | E. Byrnes |
| 18 | CLE | Cliff Lee | C. Pena |
| 19 | TEX | Linebrink | Guthrie |
| 20 | SD | Laynce Nix | Embree |
| 21 | STL | Takatso | Ainsworth |
| 22 | CLE | Chris Carpenter | Encarnacion |
| 23 | LA | Jermaine Dye | Rueter |
| 24 | STL* | Paul Wilson | D Veres |
| 25 | BOS | R Madson | Alfonzo, Eischen |
| 26 | CHI | Hafner | R Alomar |
| 27 | NY | Figgins | Catalanotto |
| 28 | OAK | Jaret Wright | Stynes |
| 29 | TEX | Biggio | Romero |
| 30 | SD | Graves | Reese |
| 31 | STL | Bellhorn | Randa |
| 32 | CLE | Inge | Fullmer |
| 33 | LA | Drese | M Byrd |
| 34 | MIN | J Rincon | |
| 35 | SD* | S Kline | Seo |
| 36 | CHI | Melhuse | J Mays |
| 37 | STL* | J Frasor | G White |
| 38 | OAK | BJ Ryan | Castro |
| 39 | TEX | D Bell | E Martinez |
| 40 | SD | Otsuka | J Jones |
| 41 | STL | Charles Thomas | O Hernandez |
| 42 | CLE | P Feliz | JJ Hardy |
| 43 | LA | L Ford | B Hill |
| 44 | MIN | J Marquis | Reitsma |
| 45 | SD* | Mirabelli | Erstad |
| 46 | CHI | C Cordero | B Mayne |
| 47 | NY | M Lawton | G Meche |
| 48 | OAK | P Byrd | Branyan |
| 49 | TEX | Nevin | Nen |
| 50 | SD | S Hairston | Hammond |
* indicates traded draft pick