| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 8 | June-Reg | John VanBenschoten | $$ | P | 21 | 4/14/1980 | 6-4 | 210 | R | R | MLB | 2004-2008 | Kent State University |
| 3 | 84** | June-Reg | Jeremy Guthrie | $$ | P | 22 | 4/8/1979 | 6-1 | 200 | B | R | MLB | 2004-2008 | Stanford University |
| 4 | 114 | June-Reg | Jeff Keppinger | | 2B | 21 | 4/21/1980 | 6-0 | 180 | R | R | MLB | 2004-2008 | University of Georgia |
| 5 | 144 | June-Reg | Travis Chapman | | 1B | 20 | 9/6/1980 | 6-1 | 205 | R | R | A+ | | Indian River Community College |
| 6 | 174 | June-Reg | Drew Friedberg | | P | 22 | 3/3/1979 | 6-2 | 200 | L | L | A | | Arizona State University |
| 7 | 204 | June-Reg | Mike McCuistion | | C | 19 | 5/14/1982 | 6-2 | 190 | L | R | A+ | | Yucaipa High School (Yucaipa,CA) |
| 8 | 234 | June-Reg | Chris Duffy | | OF | 21 | 4/20/1980 | 5-10 | 186 | B | L | MLB | 2005-2007 | Arizona State University |
| 9 | 264** | June-Reg | Jason Fellows | | 1B | 18 | 7/16/1982 | 6-3 | 173 | L | L | College | | Berkmar High School (Lilburn,GA) |
| 10 | 294** | June-Reg | Aaron Bulkley | | SS | 18 | 5/6/1983 | 6-4 | 195 | R | R | A- | | Port Byron High School (Port Byron,NY) |
| 11 | 324** | June-Reg | Stephen Drew | | SS | 18 | 3/16/1983 | 6-1 | 195 | L | R | MLB | 2006-2008 | |
| 12 | 354 | June-Reg | Tim Brown | | 1B | 18 | 2/21/1983 | 6-3 | 220 | L | L | AA | | Sheldon High School (Eugene,OR) |
| 13 | 384 | June-Reg | Jeff Dutremble | | P | 22 | 10/8/1978 | 6-2 | 195 | L | L | A- | | Dartmouth College |
| 14 | 414 | June-Reg | Jason Kiley | | P | 18 | 10/15/1982 | 6-4 | 220 | R | R | A- | | St. Charles High School (St. Charles,IL) |
| 15 | 444 | June-Reg | Jeff Miller | | P | 21 | 2/1/1980 | 6-4 | 210 | R | R | AAA | | University of New Orleans |
| 16 | 474 | June-Reg | Jon Smith | | P | | | | | | | College | | California State University, Fullerton |
| 17 | 504 | June-Reg | Tim Morley | | P | 18 | 10/27/1982 | 6-2 | 190 | L | L | College | | Adlai Stevenson High School (Lincolnshire,IL) |
| 18 | 534 | June-Reg | Lino Mariot | | SS | 18 | 10/21/1982 | 6-2 | 170 | R | R | Rookie | | Woodbridge High School (Woodbridge,NJ) |
| 19 | 564 | June-Reg | Jonathan Albaladejo | | P | 18 | 10/30/1982 | 6-5 | 210 | R | R | MLB | 2007-2008 | Miami-Dade College |
| 20 | 594 | June-Reg | Zach Duke | | P | 18 | 4/19/1983 | 6-2 | 210 | L | L | MLB | 2005-2008 | Midway High School (Hewitt,TX) |
| 21 | 624** | June-Reg | Tim Pahuta | | | 18 | 5/3/1983 | 6-4 | 225 | L | R | A | | Hunterdon Central High School (Whitehouse Station,NJ) |
| 22 | 654** | June-Reg | Jon Koch | | P | 18 | 4/7/1983 | 6-2 | 180 | R | R | Ind | | Berrien Springs High School (Berrien Springs,MI) |
| 23 | 684 | June-Reg | Casey Shumaker | | P | 20 | 7/12/1980 | 6-3 | 190 | R | R | A+ | | Jacksonville University |
| 24 | 714 | June-Reg | Marcus Davila | | P | 19 | 8/14/1981 | 6-1 | 190 | R | R | A+ | | Tallahassee Community College |
| 25 | 744 | June-Reg | Robert Coomer | | P | 20 | 10/1/1980 | 6-4 | 180 | R | R | - | | John A. Logan College |
| 26 | 774 | June-Reg | Morel Tjosandy | | P | | | | 0 | | | - | | Emerson High School (Union City,NJ) |
| 27 | 804 | June-Reg | Dan D'Amato | | P | 21 | 11/8/1979 | 6-1 | 190 | L | L | A- | | North Carolina State University |
| 28 | 834 | June-Reg | Claudell Clark | | P | 21 | 11/20/1979 | 5-10 | 187 | R | L | A- | | Norfolk State University |
| 29 | 864 | June-Reg | Scott Tower | | P | 19 | 8/19/1981 | 6-0 | 160 | L | L | A- | | Temple University |
| 30 | 894 | June-Reg | Kody Kirkland | | 3B | 18 | 6/9/1983 | 6-4 | 200 | R | R | AAA | | Pocatello High School (Pocatello,ID) |
| 31 | 924 | June-Reg | Brady Borner | | P | 22 | 4/12/1979 | 5-10 | 175 | L | L | AA | | Wayne State College (Nebraska) |
| 32 | 954** | June-Reg | Chris Torres | | C | 18 | 1/27/1983 | 6-0 | 195 | R | R | A- | | Vero Beach High School (Vero Beach,FL) |
| 33 | 984 | June-Reg | Chris Shelton | | C | 21 | 6/26/1980 | 6-0 | 200 | R | R | MLB | 2004-2008 | University of Utah |
| 34 | 1014 | June-Reg | Brett Korth | | P | 19 | 9/16/1981 | 6-4 | 200 | R | R | College | | Kishwaukee Community College |
| 35 | 1044 | June-Reg | Renardo Pitts | | CF | | | | 0 | | | - | | Jones County High School (Gray,GA) |
| 36 | 1074 | June-Reg | Adam Riddle | | | | | | | | | College | | New Mexico Junior College |
| 37 | 1104 | June-Reg | Eduardo Elias | | P | 18 | 2/17/1983 | 6-5 | 200 | R | R | College | | |
| 38 | 1134 | June-Reg | Rajai Davis | | OF | 20 | 10/19/1980 | 5-11 | 170 | B | R | MLB | 2006-2008 | University of Connecticut |
| 39 | 1164** | June-Reg | Taylor Johnson | | | 17 | 7/25/1983 | 6-0 | 195 | L | L | Ind | | Skyview High School (Vancouver,WA) |
| 40 | 1194** | June-Reg | Jase Turner | | 1B | 18 | 2/22/1983 | 6-2 | 225 | L | R | A | | Skyline High School (Oakland,CA) |
| 41 | 1223 | June-Reg | Scott Wearne | | | | | | | | | College | | Chipola College |
| 42 | 1252 | June-Reg | Preston Simms | | P | 19 | 2/13/1982 | 6-4 | 200 | R | R | Ind | | Bethany High School (Bethany,OK) |
| 43 | 1280 | June-Reg | Shane Youman | | P | 21 | 10/11/1979 | 6-4 | 205 | L | L | MLB | 2006-2007 | Louisiana State University |
| 44 | 1308** | June-Reg | Joseph Martinez | | | 18 | 2/26/1983 | 6-3 | 185 | L | R | AA | | Seton Hall Prep High School (West Orange,NJ) |
| 45 | 1336 | June-Reg | Brent Sportsman | | P | | | | 0 | | | - | | Elgin Community College |
| 46 | 1364 | June-Reg | Matt Davis | | | | | | | | | College | | Terry Parker High School (Jacksonville,FL) |
| 47 | 1392 | June-Reg | Joshua Macdonald | | | 18 | 4/21/1983 | 6-4 | 215 | R | R | College | | Notre Dame High School (Fairfield,CT) |
| 48 | 1419 | June-Reg | Tony Cekovsky | | | 18 | 10/16/1982 | 6-5 | 225 | R | R | College | | Southington High School (Southington,CT) |
| 49 | 1444 | June-Reg | Jeb Gibbs | | P | 18 | 2/24/1983 | 6-3 | 185 | R | R | - | | Pope High School (Marietta,GA) |
| 50 | 1468 | June-Reg | Justin Rethwisch | | CF | 20 | 4/5/1981 | 6-1 | 187 | L | L | Rookie | | Antelope Valley College |
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