| 1 | 8 | June-Reg | John VanBenschoten | P | 21 | 6-4 | 210 | R | R | MLB | 2004-2008 | Kent State University | $2,300,000 |
| 3 | 84** | June-Reg | Jeremy Guthrie | P | 22 | 6-1 | 200 | B | R | MLB | 2004-2009 | Stanford University | $0 |
| 4 | 114 | June-Reg | Jeff Keppinger | 2B | 21 | 6-0 | 180 | R | R | MLB | 2004-2009 | University of Georgia | $312,000 |
| 5 | 144 | June-Reg | Travis Chapman | 1B | 20 | 6-1 | 205 | R | R | A+ | | Indian River State College | $190,000 |
| 6 | 174 | June-Reg | Drew Friedberg | P | 22 | 6-2 | 200 | L | L | A | | Arizona State University | $40,000 |
| 7 | 204 | June-Reg | Mike McCuistion | C | 19 | 6-2 | 190 | L | R | A+ | | Yucaipa (Yucaipa,CA) | $220,000 |
| 8 | 234 | June-Reg | Chris Duffy | OF | 21 | 5-10 | 186 | B | L | MLB | 2005-2009 | Arizona State University | $100,000 |
| 9 | 264** | June-Reg | Jason Fellows | 1B | 18 | 6-3 | 173 | L | L | College | | Berkmar (Lilburn,GA) | |
| 10 | 294** | June-Reg | Aaron Bulkley | SS | 18 | 6-4 | 195 | R | R | A- | | Port Byron (Port Byron,NY) | |
| 11 | 324** | June-Reg | Stephen Drew | SS | 18 | 6-1 | 195 | L | R | MLB | 2006-2009 | | |
| 12 | 354 | June-Reg | Tim Brown | 1B | 18 | 6-3 | 220 | L | L | AA | | Sheldon (Eugene,OR) | |
| 13 | 384 | June-Reg | Jeff Dutremble | P | 22 | 6-2 | 195 | L | L | A- | | Dartmouth College | |
| 14 | 414 | June-Reg | Jason Kiley | P | 18 | 6-4 | 220 | R | R | A- | | St. Charles (St. Charles,IL) | |
| 15 | 444 | June-Reg | Jeff Miller | P | 21 | 6-4 | 210 | R | R | AAA | | University of New Orleans | |
| 16 | 474 | June-Reg | Jon Smith | P | 22 | 6-0 | 200 | L | L | College | | Cal State Fullerton | |
| 17 | 504 | June-Reg | Tim Morley | P | 18 | 6-2 | 190 | L | L | College | | Stevenson (Lincolnshire,IL) | |
| 18 | 534 | June-Reg | Lino Mariot | SS | 18 | 6-2 | 170 | R | R | Ind | | Woodbridge (Woodbridge,NJ) | |
| 19 | 564 | June-Reg | Jonathan Albaladejo | P | 18 | 6-5 | 210 | R | R | MLB | 2007-2009 | Miami-Dade College | |
| 20 | 594 | June-Reg | Zach Duke | P | 18 | 6-2 | 210 | L | L | MLB | 2005-2009 | Midway (Waco,TX) | |
| 21 | 624** | June-Reg | Tim Pahuta | | 18 | 6-4 | 225 | L | R | A+ | | Hunterdon Central (Whitehouse Station,NJ) | |
| 22 | 654** | June-Reg | Jon Koch | P | 18 | 6-2 | 180 | R | R | Ind | | Berrien Springs (Berrien Springs,MI) | |
| 23 | 684 | June-Reg | Casey Shumaker | P | 20 | 6-3 | 190 | R | R | A+ | | Jacksonville University | |
| 24 | 714 | June-Reg | Marcus Davila | P | 19 | 6-1 | 190 | R | R | A+ | | Tallahassee Community College | |
| 25 | 744 | June-Reg | Robert Coomer | P | 20 | 6-4 | 180 | R | R | - | | John A. Logan College | |
| 26 | 774 | June-Reg | Morel Tjosandy | P | | | 0 | | | - | | Emerson (Union City,NJ) | |
| 27 | 804 | June-Reg | Dan D'Amato | P | 21 | 6-1 | 190 | L | L | A- | | North Carolina State University | |
| 28 | 834 | June-Reg | Claudell Clark | P | 21 | 5-10 | 187 | R | L | A- | | Norfolk State University | |
| 29 | 864 | June-Reg | Scott Tower | P | 19 | 6-0 | 160 | L | L | A- | | Temple University | |
| 30 | 894 | June-Reg | Kody Kirkland | 3B | 18 | 6-4 | 200 | R | R | AAA | | Pocatello (Pocatello,ID) | |
| 31 | 924 | June-Reg | Brady Borner | P | 22 | 5-10 | 175 | L | L | AA | | Wayne State College (Nebraska) | |
| 32 | 954** | June-Reg | Chris Torres | C | 18 | 6-0 | 195 | R | R | A- | | Vero Beach (Vero Beach,FL) | |
| 33 | 984 | June-Reg | Chris Shelton | C | 21 | 6-0 | 200 | R | R | MLB | 2004-2009 | University of Utah | |
| 34 | 1014 | June-Reg | Brett Korth | P | 19 | 6-4 | 200 | R | R | College | | Kishwaukee College | |
| 35 | 1044 | June-Reg | Renardo Pitts | CF | | | 0 | | | - | | Jones County (Gray,GA) | |
| 36 | 1074 | June-Reg | Adam Riddle | | | | | | | College | | New Mexico Junior College | |
| 37 | 1104 | June-Reg | Eduardo Elias | P | 18 | 6-5 | 200 | R | R | College | | | |
| 38 | 1134 | June-Reg | Rajai Davis | OF | 20 | 5-11 | 170 | R | R | MLB | 2006-2009 | University of Connecticut | |
| 39 | 1164** | June-Reg | Taylor Johnson | | 17 | 6-0 | 195 | L | L | Ind | | Skyview (Vancouver,WA) | |
| 40 | 1194** | June-Reg | Jase Turner | 1B | 18 | 6-2 | 225 | L | R | A | | Skyline (Oakland,CA) | |
| 41 | 1223 | June-Reg | Scott Wearne | | | | | | | College | | Chipola College | |
| 42 | 1252 | June-Reg | Preston Simms | P | 19 | 6-4 | 200 | R | R | Ind | | Bethany (Bethany,OK) | |
| 43 | 1280 | June-Reg | Shane Youman | P | 21 | 6-4 | 205 | L | L | MLB | 2006-2007 | Louisiana State University | |
| 44 | 1308** | June-Reg | Joe Martinez | | 18 | 6-3 | 185 | L | R | MLB | 2009-2009 | Seton Hall Prep (West Orange,NJ) | |
| 45 | 1336 | June-Reg | Brent Sportsman | P | | | 0 | | | - | | Elgin Community College | |
| 46 | 1364 | June-Reg | Matt Davis | | | | | | | College | | Terry Parker (Jacksonville,FL) | |
| 47 | 1392 | June-Reg | Joshua Macdonald | | 18 | 6-4 | 215 | R | R | College | | Notre Dame (Fairfield,CT) | |
| 48 | 1419 | June-Reg | Tony Cekovsky | | 18 | 6-5 | 225 | R | R | College | | Southington (Southington,CT) | |
| 49 | 1444 | June-Reg | Jeb Gibbs | P | 18 | 6-3 | 185 | R | R | - | | Pope (Marietta,GA) | |
| 50 | 1468 | June-Reg | Justin Rethwisch | CF | 20 | 6-1 | 187 | L | L | Rookie | | Antelope Valley College | |