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| 2007 |
2006 |
2005 |
2004 |
2003 |
| Pick # | Drafted By | Player | Dropped Player(s) |
| 1 | TEX | Justin Upton | Munson |
| 2 | STL* | Brady Clark | Spivey |
| 3 | NY* | Bruce Chen | |
| 4 | STL | Huston Street | Sleeth |
| 5 | NY | Felipe Lopez | |
| 6 | CHI | Chris Young | J. Gonzalez |
| 7 | CLE | Jorge Cantu | Jenkins |
| 8 | LA | Jesse Crain | Dan Wilson |
| 9 | NY* | David Dellucci | Brian Anderson |
| 10 | BOS | John Patterson | Hidalgo |
| 11 | TEX | Eric Bedard | Stokes |
| 12 | NY* | Nate Robertson | F. Gutierrez |
| 13 | NY* | Scott Olson | Hee Seop Choi |
| 14 | STL | Zack Duke | Charles Thomas |
| 15 | NY | Chacin | |
| 16 | CHI | Chris Capuano | B. Santiago |
| 17 | CLE | Jeff Francoeur | D. Cabrera |
| 18 | LA | Barmes | Clayton |
| 19 | BOS* | Adam Kennedy | Rivas |
| 20 | BOS | Politte | R. Wagner |
| 21 | LA | Wang | Madritsch |
| 22 | CHI | Dustin Hermanson | Davanon |
| 23 | CLE | Bill Hall | Marrero |
| 24 | STL | Brandon Wood (LAA) | Halama |
| 25 | LA* | DeJesus | Holliday |
| 26 | MIN | B. Moehler | Milton |
| 27 | NY* | R. Freel | Lugo |
| 28 | TEX | Mark Redman | Olerud |
| 29 | OAK | Randa | Koch |
| 30 | BOS | Connor Jackson | Dotel |
| 31 | LA | Jose Castillo | Cuddyer |
| 32 | CHI | Chris Shelton | Nomo |
| 33 | CLE | Dan Wheeler | Shouse |
| 34 | STL | DJ Carrasco | Paul Wilson |
| 35 | NY | Matt Miller | Chad Bradford |
| 36 | NY* | Todd Jones | Bernie Williams |
| 37 | NY* | Mackowiak | Monroe |
| 38 | TEX | Turnbow | Mondesi |
| 39 | OAK | Rhodes | Meintkiewicz |
| 40 | BOS | Quentin | Bagwell |
| 41 | LA | Juan Encarnacion | L. Ford |
| 42 | CHI | Church | Darrel May |
| 43 | CLE | Andy LaRoche | Infante |
| 44 | STL | Mike LaPorte(U-FLA) | Wigginton |
| 45 | NY | Gregg Zaun | Tony Armas, Jr. |
| 46 | MIN | Sisco | Jose Valentin, Redding |
| 47 | STL* | Alex Gordon (U-Neb) | Vargas |
| 48 | TEX | Nady | Dessens |
| 49 | OAK | Al Reyes | Payton |
| 50 | BOS | McCann | K. Brown |
* indicates traded draft pick
(San Diego drops Charles Johnson, C, Colorado)