Link to detailed top 40 prospects article on Scout.com.
| 1 | Colby Rasmus |
| 2 | Blake Hawksworth |
| 3 | Jaime Garcia |
| 4 | Bryan Anderson |
| 5 | Adam Ottavino |
| 6 | Chris Narveson |
| 7 | Stuart Pomeranz |
| 8 | Chris Perez |
| 9 | Jon Jay |
| 10 | Nick Stavinoha |
| 11 | Mark McCormick |
| 12 | Cody Haerther |
| 13 | Josh Kinney |
| 14 | Chris Lambert |
| 15 | Jon Edwards |
| 16 | Tyler Greene |
| 17 | Daryl Jones |
| 18 | Mark Hamilton |
| 19 | Brendan Ryan |
| 20 | Tyler Herron |
| 21 | Mitchell Boggs |
| 22 | Blake King |
| 23 | Amaury Marti |
| 24 | Mark Worrell |
| 25 | Mike Parisi |
| 26 | Nick Webber |
| 27 | Andy Cavazos |
| 28 | Mike Sillman |
| 29 | Eric Haberer |
| 30 | Jose Martinez |
| 31 | Tyler Norrick |
| 32 | Eddie Degerman |
| 33 | Dennis Dove |
| 34 | Randy Roth |
| 35 | Gary Daley |
| 36 | Donovan Solano |
| 37 | Isa Garcia |
| 38 | Skip Schumaker |
| 39 | Tommy Pham |
| 40 | Cory Meacham |