| Round | Pick | Team | Selection | Pos, '03 Team |
| 1 | 1 | Toronto | Hudson, Tim | P, Oakland |
| 1 | 2 | New York (NL) | Beckett, Josh | P, Florida |
| 1 | 3 | Milwaukee | Vazquez, Javier | P, Montreal |
| 1 | 4 | Colorado | Sheffield, Gary | OF, Atlanta |
| 1 | 5 | Baltimore | Beltran, Carlos | OF, Kansas City |
| 2 | 1 | Baltimore | Thome, Jim | 1B, Philadelphia |
| 2 | 2 | Colorado | Posada, Jorge | C, New York (AL) |
| 2 | 3 | Milwaukee | Jeter, Derek | SS, New York (AL) |
| 2 | 4 | New York (NL) | Wells, Vernon | OF, Toronto |
| 2 | 5 | Toronto | Furcal, Rafael | SS, Atlanta |
| 3 | 1 | Toronto | Miller, Wade | P, Houston |
| 3 | 2 | New York (NL) | Reyes, Jose | SS, New York (NL) |
| 3 | 3 | Milwaukee | Ensberg, Morgan | 3B, Houston |
| 3 | 4 | Colorado | Ortiz, David | 1B, Boston |
| 3 | 5 | Baltimore | Crawford, Carl | OF, Tampa Bay |
| 4 | 1 | Baltimore | Maddux, Greg | P, Atlanta |
| 4 | 2 | Colorado | Polanco, Placido | 2B, Philadelphia |
| 4 | 3 | Milwaukee | Lowe, Derek | P, Boston |
| 4 | 4 | New York (NL) | Cintron, Alex | SS, Arizona |
| 4 | 5 | Toronto | Marte, Damaso | P, Chicago (AL) |
| 5 | 1 | Toronto | Bigbie, Larry | OF, Baltimore |
| 5 | 2 | New York (NL) | Hinske, Eric | 3B, Toronto |
| 5 | 3 | Milwaukee | Ohka, Tomo | P, Montreal |
| 5 | 4 | Colorado | Hampton, Mike | P, Atlanta |
| 5 | 5 | Baltimore | Hudson, Orlando | 2B, Toronto |
| 6 | 1 | Baltimore | Urbina, Ugueth | P, Florida |
| 6 | 2 | Colorado | Wells, David | P, New York (AL) |
| 6 | 3 | Milwaukee | Molina, Ben | C, Anaheim |
| 6 | 4 | New York (NL) | Cordero, Francisco | P, Texas |
| 6 | 5 | Toronto | Gibbons, Jay | OF, Baltimore |
| 7 | 1 | Toronto | Castilla, Vinny | 3B, Atlanta |
| 7 | 2 | New York (NL) | Lecroy, Matt | C, Minnesota |
| 7 | 3 | Milwaukee | Jones, Jacque | OF, Minnesota |
| 7 | 4 | Colorado | Chacon, Shawn | P, Colorado |
| 7 | 5 | Baltimore | Riske, David | P, Cleveland |
| 8 | 1 | Baltimore | Mondesi, Raul | OF, Arizona |
| 8 | 2 | Colorado | Hawkins, LaTroy | P, Minnesota |
| 8 | 3 | Milwaukee | Grudzielanek, Mark | 2B, Chicago (NL) |
| 8 | 4 | New York (NL) | Perez, Oliver | P, Pittsburgh |
| 8 | 5 | Toronto | Redmond, Mike | C, Florida |
| 9 | 1 | Toronto | Rueter, Kirk | P, San Francisco |
| 9 | 2 | New York (NL) | Davis, Jason | P, Cleveland |
| 9 | 3 | Milwaukee | Guzman, Cristian | SS, Minnesota |
| 9 | 4 | Colorado | Lugo, Julio | SS, Tampa Bay |
| 9 | 5 | Baltimore | Armas Jr., Tony | P, Montreal |
| 10 | 1 | Baltimore | Millar, Kevin | OF, Boston |
| 10 | 2 | Colorado | Guardado, Eddie | P, Minnesota |
| 10 | 3 | Milwaukee | Olerud, John | 1B, Seattle |
| 10 | 4 | New York (NL) | Helms, Wes | 3B, Milwaukee |
| 10 | 5 | Toronto | Burnitz, Jeromy | OF, Los Angeles |