| 1 | 16 | June-Reg | Nick Swisher | OF | 21 | 6-0 | 200 | B | L | MLB | 2004-2009 | Ohio State University | $1,780,000 |
| 1 | 24 | June-Reg | Joe Blanton | P | 21 | 6-2 | 220 | R | R | MLB | 2004-2009 | University of Kentucky | $1,400,000 |
| 1 | 26 | June-Reg | John McCurdy | IF | 21 | 6-2 | 200 | R | R | AA | | University of Maryland | |
| 1 | 30 | June-Reg | Ben Fritz | P | 21 | 6-4 | 225 | R | R | AAA | | Fresno State University | |
| 1 | 35 | June-Reg | Jeremy Brown | C | 22 | 5-10 | 210 | R | R | MLB | 2006-2006 | University of Alabama | |
| 1 | 37 | June-Reg | Steve Obenchain | P | 20 | 6-5 | 220 | R | R | AA | | University of Evansville | |
| 1 | 39 | June-Reg | Mark Teahen | 3B | 20 | 6-3 | 210 | L | R | MLB | 2005-2009 | St. Mary's College of California | $750,000 |
| 2 | 67 | June-Reg | Steve Stanley | OF | 22 | 5-8 | 155 | L | L | AAA | - | University of Notre Dame | |
| 3 | 98 | June-Reg | Bill Murphy | P | 21 | 6-0 | 190 | L | L | MLB | 2007-2009 | University of California-Riverside | |
| 4 | 128 | June-Reg | John Baker | C | 21 | 6-1 | 220 | L | R | MLB | 2008-2009 | University of California | |
| 5 | 158 | June-Reg | Mark Kiger | IF | 22 | 5-11 | 177 | R | R | AAA | | University of Florida | |
| 6 | 188 | June-Reg | Brian Stavisky | OF | 21 | 6-3 | 220 | L | R | AAA | | University of Notre Dame | |
| 7 | 218 | June-Reg | Brant Colamarino | 1B | 21 | 5-11 | 200 | L | L | AAA | | University of Pittsburgh | |
| 8 | 248 | June-Reg | Jared Burton | P | 21 | 6-5 | 220 | R | R | MLB | 2007-2009 | Western Carolina University | |
| 9 | 278 | June-Reg | Shane Komine | P | 21 | 5-8 | 160 | R | R | MLB | 2006-2007 | University of Nebraska | |
| 10 | 308 | June-Reg | J.R. Pickens | P | 22 | 6-1 | 210 | L | R | A+ | | University of Mississippi | |
| 11 | 338 | June-Reg | Justin Crowder | P | 22 | 6-0 | 190 | L | L | AA | | Rice University | |
| 12 | 368 | June-Reg | Kirk Nordness | OF | 22 | 6-0 | 200 | R | R | A | | Armstrong Atlantic State University | |
| 13 | 398 | June-Reg | Tyler Klippenstein | 1B | 21 | 6-4 | 210 | R | R | A- | | University of Lethbridge | |
| 14 | 428 | June-Reg | Brad Knox | P | 20 | 6-3 | 210 | R | R | AAA | | Central Arizona College | |
| 15 | 458 | June-Reg | Chris Dunwell | P | 22 | 6-1 | 200 | R | R | A+ | | San Diego State University | |
| 16 | 488 | June-Reg | Lloyd Turner | IF | 22 | 6-1 | 180 | R | R | AAA | | Kennesaw State University | |
| 17 | 518 | June-Reg | David Harriman | C | 21 | 6-0 | 200 | R | R | A+ | | Armstrong Atlantic State University | |
| 18 | 548 | June-Reg | Jose Corchado | P | 18 | 6-0 | 190 | R | R | A+ | | Hilberto Domenech (Isabela,PR) | |
| 19 | 578** | June-Reg | Dusty Barnard | P | 19 | 6-2 | 200 | R | R | College | | Moore (Moore,OK) | |
| 20 | 608** | June-Reg | Trevor Crowe | SS | 18 | 6-0 | 190 | B | R | MLB | 2009-2009 | Westview (Portland,OR) | $0 |
| 21 | 638 | June-Reg | Wally Pontiff | | | | | | | College | | Louisiana State University | |
| 22 | 668 | June-Reg | Shawn Kohn | P | 22 | 6-2 | 200 | R | R | AAA | | University of Washington | |
| 23 | 698 | June-Reg | Chris Shank | P | 21 | 6-1 | 180 | R | R | A+ | | Franklin Pierce University | |
| 24 | 728 | June-Reg | Danny Gibbons | OF | 21 | 6-3 | 200 | L | L | A | | Central Michigan University | |
| 25 | 758 | June-Reg | Steve Schilsky | P | 21 | 6-2 | 210 | R | R | A- | | Illinois Wesleyan University | |
| 26 | 788 | June-Reg | Ty Bubalo | C | 18 | 6-3 | 205 | R | R | A- | | Beaverton (Beaverton,OR) | |
| 27 | 818 | June-Reg | Greg Dupas | P | 18 | 6-8 | 230 | R | R | A+ | | Arlington (Riverside,CA) | |
| 28 | 848 | June-Reg | Andy Dickinson | P | 22 | 6-2 | 170 | L | L | AA | | University of Illinois | |
| 29 | 878 | June-Reg | Danny Barnett | P | 19 | 6-0 | 190 | R | R | A- | | Salt Lake Community College | |
| 30 | 908 | June-Reg | Brian Rodgers | CF | 18 | 6-4 | 190 | R | R | - | | Berkmar (Lilburn,GA) | |
| 31 | 938** | June-Reg | Brad Ziegler | P | 22 | 6-4 | 200 | R | R | MLB | 2008-2009 | Missouri State University | |
| 32 | 968** | June-Reg | J.R. Towles | C | 18 | 6-2 | 190 | R | R | MLB | 2007-2009 | Crosby (Crosby,TX) | |
| 33 | 998 | June-Reg | Nathaniel Nelson | 1B | | | 0 | | | Rookie | | Holy Name Central (Worcester,MA) | |
| 34 | 1028 | June-Reg | Rene Quintana | SS | | | 0 | | | Ind | | Patria La Torres Ramirez (San Sebastian,PR) | |
| 35 | 1058 | June-Reg | Robert Jacobson | C | 17 | 6-1 | 205 | B | R | - | | Durango (Las Vegas,NV) | |
| 36 | 1088 | June-Reg | Jed Morris | C | 22 | 5-11 | 190 | L | R | AAA | | University of Nebraska | |
| 37 | 1118 | June-Reg | Mark Rodrigues | P | 19 | 6-2 | 165 | L | R | A+ | | Los Medanos College | |
| 38 | 1148 | June-Reg | Jason Williams | P | | | 0 | | | - | | Cactus Shadows (Cave Creek,AZ) | |
| 39 | 1178 | June-Reg | Joel Evans | P | | | 0 | | | - | | Columbia Basin College | |
| 40 | 1208** | June-Reg | Jonathan Papelbon | | 21 | 6-4 | 220 | R | R | MLB | 2005-2009 | Mississippi State University | $0 |
| 41 | 1238 | June-Reg | Don Sutton | 1B | 18 | 6-0 | 225 | R | R | A+ | | Durango (Las Vegas,NV) | |
| 42 | 1268 | June-Reg | Joe Ryan | P | | | 0 | | | - | | Assumption (Davenport,IA) | |
| 43 | 1297** | June-Reg | Curtis White | P | 21 | 5-11 | 180 | L | L | College | | University of Oklahoma | |
| 44 | 1325** | June-Reg | Ty Taubenheim | P | 19 | 6-5 | 235 | R | R | MLB | 2006-2008 | Edmonds Community College | |
| 45 | 1352 | June-Reg | Matt Elfeldt | | 21 | 6-3 | 185 | R | R | Ind | | Boston College | |
| 46 | 1362 | June-Reg | Fernando De Aza | P | 21 | 6-3 | 200 | R | R | Ind | | Wabash Valley College | |