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| 2007 |
2006 |
2005 |
2004 |
2003 |
| Pick # | Drafted By | Player | Dropped Player(s) |
| 1 | TEX | Hunter Pence | Javy Lopez |
| 2 | LA | Carlos Pena | Kip Wells |
| 3 | NY* | Jarrod Saltalamacchia | - |
| 4 | NY* | Ian Snell | Callaspo |
| 5 | MIN | Yovani Gallardo | Craig Wilson |
| 6 | NY | Dustin Pedroia | Maroth |
| 7 | MIN* | Jeremy Guthrie | (Preston Wilson)! |
| 8 | STL | Tom Gorzalanny | Lieberthal |
| 9 | CHI | Aaron Rowand | Barajas |
| 10 | BOS | Placido Polanco | John Patterson |
| 11 | TEX | Matt Guerrier | Vidro |
| 12 | LA | Olliver Perez | Nixon |
| 13 | SD | Brandon League | MacDougal |
| 14 | CLE | Corey Hart | Horacio Ramirez, Aaron Cook |
| 15 | MIN | Travis Buck | Jack Wilson |
| 16 | NY | James Shields | Coco Crisp |
| 17 | TEX* | Hideki Okajima | Biggio |
| 18 | STL | Sergio Mitre | Julio Lugo |
| 19 | CHI | Fausto Carmona | Kotsay |
| 20 | BOS | John Buck | Mike Piazza |
| 21 | STL | Andrew Miller | Austin Kearns |
| 22 | NY | Jack Cust | Adam Loewen |
| 23 | MIN | Eric Gagne | Andrew Sisco |
| 24 | SD* | Jay Bruce | Jason Larue |
| 25 | TEX | Clayton Kershaw | Livan Hernandez |
| 26 | MIN* | Heath Bell | Tomo Ohka |
| 27 | SD | Scott Cassidy | Jeff Weaver |
| 28 | CLE | Akinori Iwamura | Wily Mo Pena |
| 29 | CHI | Marlon Byrd | Loiaza |
| 30 | *CLE | Josh Fields | Ensberg |
| 31 | STL | Brandon League | Dallas McPherson |
| 32 | NY | Mike Lamb | Ben Broussard |
| 33 | MIN | Dmitri Young | - |
| 34 | NY* | Ryan Franklin | David Dellucci |
| 35 | TEX | Kevin Slowey | Randy Johnson |
| 36 | OAK | Ted Lilly | Aubrey Huff |
| 37 | SD | Chris Sampson | Benitez, Brad Thompson |
| 38 | CLE* | Y. Betancourt | Bartolo Colon |
| 39 | CHI | Rich Hill | Donnally |
| 40 | BOS | Jacoby Ellsbury | Bobby Crosby |
| 41 | STL | Ty Wigginton | Clement |
| 42 | NY | Casey Jannsen | Mark Prior |
| 43 | OAK* | Tony Pena (RP) | Mike Sweeney |
| 44 | LA | Darren Oliver | Roberto Hernandez |
| 45 | STL* | Carlos Villanueva | Brandon Wood |
| 46 | SD* | Chris Coste | Jeff Mathis |
| 47 | SD | Ryan Theriot | Brad Ausmus |
| 48 | CLE | Joe Kennedy | Andy Marte |
| 49 | CHI | Kelly Shoppach | Mark Mulder |
| 50 | NY* | Neil Walker | Jonny Gomes |
* indicates traded draft pick