| Round | Pick | Team | Selection | Pos, '03 Team |
| 11 | 1 | Toronto | Ortiz, Ramon | P, Anaheim |
| 11 | 2 | New York (NL) | Sanchez, Freddy | 2B, Pittsburgh |
| 11 | 3 | Milwaukee | Gonzalez, Juan | OF, Texas |
| 11 | 4 | Colorado | Quantrill, Paul | P, Los Angeles |
| 11 | 5 | Baltimore | Rincon, Juan | P, Minnesota |
| 12 | 1 | Baltimore | Hendrickson, Mark | P, Toronto |
| 12 | 2 | Colorado | Reed, Rick | P, Minnesota |
| 12 | 3 | Milwaukee | Carter, Lance | P, Tampa Bay |
| 12 | 4 | New York (NL) | Maroth, Mike | P, Detroit |
| 12 | 5 | Toronto | Alou, Moises | OF, Chicago (NL) |
| 13 | 1 | Toronto | Bennett, Gary | C, Milwaukee |
| 13 | 2 | New York (NL) | Rowand, Aaron | OF, Chicago (AL) |
| 13 | 3 | Milwaukee | Perez, Eddie | C, Milwaukee |
| 13 | 4 | Colorado | White, Rondell | OF, Kansas City |
| 13 | 5 | Baltimore | Weber, Ben | P, Anaheim |
| 14 | 1 | Baltimore | Zaun, Gregg | C, Colorado |
| 14 | 2 | Colorado | DaVanon, Jeff | OF, Anaheim |
| 14 | 3 | Milwaukee | Schoeneweis, Scott | P, Chicago (AL) |
| 14 | 4 | New York (NL) | Marrero, Eli | OF, St. Louis |
| 14 | 5 | Toronto | Graffanino, Tony | SS, Chicago (AL) |
| 15 | 1 | Toronto | Hatteberg, Scott | 1B, Oakland |
| 15 | 2 | New York (NL) | Figgins, Chone | OF, Anaheim |
| 15 | 3 | Milwaukee | Guiel, Aaron | OF, Kansas City |
| 15 | 4 | Colorado | Weathers, Dave | P, New York (NL) |
| 15 | 5 | Baltimore | Koch, Billy | P, Chicago (AL) |
| 16 | 1 | Baltimore | Cruz, Ivan | 1B, St. Louis |
| 16 | 2 | Colorado | Michaels, Jason | OF, Philadelphia |
| 16 | 3 | Milwaukee | Rolls, Damian | 3B, Tampa Bay |
| 16 | 4 | New York (NL) | Rodriguez, Felix | P, San Francisco |
| 16 | 5 | Toronto | Rincon, Ricardo | P, Oakland |
| 17 | 1 | Toronto | Sele, Aaron | P, Anaheim |
| 17 | 2 | New York (NL) | Branyan, Russell | 3B, Cincinnati |
| 17 | 3 | Milwaukee | Lopez, Rodrigo | P, Baltimore |
| 17 | 4 | Colorado | Stynes, Chris | 3B, Colorado |
| 17 | 5 | Baltimore | Cruz, Jacob | OF, Detroit |
| 18 | 1 | Baltimore | Higginson, Bobby | OF, Detroit |
| 18 | 2 | Colorado | Stephenson, Garrett | P, St. Louis |
| 18 | 3 | Milwaukee | Simon, Randall | 1B, Chicago (NL) |
| 18 | 4 | New York (NL) | Cordero, Wil | 1B, Montreal |
| 18 | 5 | Toronto | Wilson, Vance | C, New York (NL) |
| 19 | 1 | Toronto | Kline, Steve | P, St. Louis |
| 19 | 2 | New York (NL) | Asencio, Miguel | P, Kansas City |
| 19 | 3 | Milwaukee | Ford, Lew | OF, Minnesota |
| 19 | 4 | Colorado | Anderson, Marlon | 2B, Tampa Bay |
| 19 | 5 | Baltimore | Hyzdu, Adam | OF, Pittsburgh |
| 20 | 1 | Baltimore | Jackson, Ryan | OF, Detroit |
| 20 | 2 | Colorado | Surhoff, B.J. | OF, Baltimore |
| 20 | 3 | Milwaukee | Martinez, Tino | 1B, St. Louis |
| 20 | 4 | New York (NL) | Sullivan, Scott | P, Chicago (AL) |
| 20 | 5 | Toronto | Erstad, Darin | OF, Anaheim |
| 21 | 1 | Toronto | Blum, Geoff | 3B, Houston |
| 21 | 2 | New York (NL) | Wright, Dan | P, Chicago (AL) |
| 21 | 3 | Milwaukee | Hermanson, Dustin | P, San Francisco |
| 21 | 4 | Colorado | Reed, Steve | P, Colorado |
| 21 | 5 | Baltimore | Condrey, Clay | P, San Diego |
| 22 | 1 | Baltimore | Gryboski, Kevin | P, Atlanta |
| 22 | 2 | Colorado | Werth, Jayson | OF, Toronto |
| 22 | 3 | Milwaukee | Eischen, Joey | P, Montreal |
| 22 | 4 | New York (NL) | Reese, Pokey | 2B, Pittsburgh |
| 22 | 5 | Toronto | Reynolds, Shane | P, Atlanta |