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| Pick | Name | Pos | School |
| 18 | Josh Fields | 3B | Oklahoma St. |
| 34 | Tyler Lumsden | LHP | Clemson |
| 38 | Giovanny Gonzalez | LHP | Miami Monsignor Pace HS |
| 53 | Wes Whisler | LHP/1B | UCLA |
| 59 | Donald Lucy | C | Stanford |
| 69 | Ray Liotta | LHP | Gulf Coast CC |
| 89 | Grant Hansen | RHP | Oklahoma City |
| 119 | Lucas Harrell | RHP | Ozark HS (Mo.) |
| 149 | Brandon Allen | OF/1B | Montgomery HS (Texas) |
| 179 | Adam Russell | RHP | Ohio University |
| 209 | Timothy Murphey | RHP | Glascock County HS (Ga.) |
| 239 | Nick Lemon | RHP | BYU |
| 269 | Ryan McCarthy | SS | California |
| 299 | Adam Ricks | 3B | Miami (Fla.) |
| 329 | Garry Bakker | RHP | North Carolina |
| 359 | Daron Roberts | CF | California State |
| 389 | Jack Egbert | RHP | Rutgers |
| 419 | Michael Swain | 3B | Wabash Valley |
| 449 | Carlos Torres | RHP | Kansas State |
| 479 | Fernando Alvarez | OF | Fla. International |
| 509 | Jacob Wild | RHP | Bakersfield CC |
| 539 | Brett Scarpetta | RHP | Rockton Hononegah HS |
| 569 | Caleb Cooper | 3B | Cal St. Hayward |
| 599 | Michael Dubee | RHP | Riverview HS |
| 629 | Brian Flores | LHP | Carlsbad HS |
| 659 | Matthew Mansilla | SS | American Heritage |
| 689 | Derek McNeil | SS | St. Leo College |
| 719 | Joshua Hansen | C | San Diego |
| 749 | Justin Sincock | RHP | Millikan HS |
| 779 | Daniel Jordan | 3B | Gulliver Prep |
| 809 | Logan Williamson | LHP | Pensacola CC |
| 839 | Gregory Young | CF | Delaware Tech CC |
| 869 | Frank Viola | RHP | Florida CC |
| 899 | Kyle Zaleski | RHP | Indiana St. |
| 929 | Nichols Walters | LHP | Mountian Ridge HS |
| 959 | Eric Sheridan | RHP | Saddleback CC |
| 989 | Brandon Cooney | RHP | Broward CC |
| 1019 | Mario Suarez | 3B | Fla. International |
| 1049 | Evan Tartaglia | CF | Elon |
| 1079 | Ken Williams | CF | Plainfield HS |
| 1109 | Robert Grinestaff | C | Okaloosa Walton CC |
| 1139 | Shaun Spearman | SS | St. Pius X HS |
| 1169 | James Leigh | LHP | Bryant HS |
| 1199 | James Roelle | LHP | Iowa Western CC |
| 1229 | Matthew Rozier | RHP | Meridian CC |
| 1258 | Michael Schower | LHP | Riverview HS |
| 1287 | Ian Murray | RHP | Jefferson College |
| 1316 | Steve Muck | RHP | Covington Catholic HS |
| 1345 | Jason Sullivan | RHP | Crowder JC |
| 1374 | Jason Rodriguez | SS | Alta Loma HS |
| 1403 | Richard O’Brien | C | — |
| 1432 | Peter Vuckovich | C | Clarion |
| 1460 | Dennis Guest | 2B | St. Joseph |
| 1488 | Bryan Wagner | RHP | Thunderbird HS |
