Link to top 40 prospect articles at Scout.com.
| 1 | Colby Rasmus |
| 2 | Bryan Anderson |
| 3 | Jaime Garcia |
| 4 | Chris Perez |
| 5 | Adam Ottavino |
| 6 | Tyler Herron |
| 7 | Jose Martinez |
| 7a | Brian Barton |
| 8 | Joe Mather |
| 9 | Clayton Mortensen |
| 10 | P.J. Walters |
| 11 | Allen Craig |
| 12 | Mark Hamilton |
| 13 | Mitchell Boggs |
| 13a | David Freese |
| 14 | Jarrett Hoffpauir |
| 15 | Kenny Maiques |
| 16 | Pete Kozma |
| 17 | Tyler Greene |
| 18 | Jess Todd |
| 19 | Jon Jay |
| 20 | Mark McCormick |
| 21 | Josh Kinney |
| 22 | Jason Motte |
| 23 | Blake Hawksworth |
| 24 | Luke Gregerson |
| 25 | Jon Edwards |
| 26 | Tyler Norrick |
| 27 | Cody Haerther |
| 28 | Luis de la Cruz |
| 29 | Stuart Pomeranz |
| 30 | Brad Furnish |
| 31 | Kyle McClellan |
| 32 | Deryk Hooker |
| 33 | Mark Worrell |
| 34 | Blake King |
| 35 | Mike Parisi |
| 36 | David Kopp |
| 37 | Brandon Buckman |
| 38 | Nick Stavinoha |
| 39 | D’Marcus Ingram |
| 40 | Steven Hill |