| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 22 | June-Reg | David Aardsma | $$ | P | 21 | 12/27/1981 | 6-5 | 200 | R | R | MLB | 2004-2008 | Rice University |
| 1 | 34 | June-Reg | Craig Whitaker | $$ | P | 18 | 11/19/1984 | 6-4 | 170 | R | R | AA | | Lufkin High School (Lufkin,TX) |
| 2 | 55 | June-Reg | Todd Jennings | $$ | C | 21 | 12/10/1981 | 6-0 | 190 | R | R | AAA | | Long Beach State University |
| 2 | 63 | June-Reg | Nate Schierholtz | $$ | 3B | 19 | 2/15/1984 | 6-2 | 215 | L | R | MLB | 2007-2007 | Chabot College |
| 3 | 93 | June-Reg | Brian Buscher | $$ | 3B | 22 | 4/18/1981 | 6-0 | 185 | L | R | MLB | 2007-2008 | University of South Carolina |
| 4 | 123 | June-Reg | Brooks McNiven | | P | 22 | 6/19/1981 | 6-5 | 180 | R | R | AAA | | University of British Columbia |
| 5 | 153 | June-Reg | Mike Wagner | | OF | 21 | 9/13/1981 | 6-3 | 210 | R | R | AA | | University of Washington |
| 6 | 183 | June-Reg | Billy Sadler | | P | 21 | 9/21/1981 | 6-0 | 190 | R | R | MLB | 2006-2008 | Louisiana State University |
| 7 | 213 | June-Reg | Pat Misch | | P | 21 | 8/18/1981 | 6-2 | 170 | R | L | MLB | 2006-2008 | Western Michigan University |
| 8 | 243 | June-Reg | Tim Hutting | | SS | 21 | 10/29/1981 | 6-0 | 190 | R | R | AAA | | Long Beach State University |
| 9 | 273 | June-Reg | Kellen Ludwig | | P | 20 | 11/19/1982 | 6-4 | 230 | R | R | A- | | Chipola College |
| 10 | 303 | June-Reg | Jesse Schmidt | | OF | 21 | 10/27/1981 | 6-1 | 200 | B | R | A | | Cal State Sacramento |
| 11 | 333 | June-Reg | Jeff Petersen | | P | 21 | 10/16/1981 | 6-4 | 225 | R | R | AAA | | University of Washington |
| 12 | 363 | June-Reg | Ryan Sadowski | | P | 20 | 10/4/1982 | 6-3 | 185 | R | R | AAA | | University of Florida |
| 13 | 393 | June-Reg | Nick Conte | | C | 21 | 1/25/1982 | 5-10 | 175 | R | R | A | | St. Mary's College of California |
| 14 | 423 | June-Reg | Sean Martin | | P | 23 | 3/27/1980 | 6-1 | 190 | R | R | A+ | | California State University, Fullerton |
| 15 | 453 | June-Reg | Ben Thurmond | | P | 21 | 10/2/1981 | 6-0 | 190 | R | R | A+ | | Arizona State University |
| 16 | 483 | June-Reg | Mike Mooney | | OF | 20 | 6/8/1983 | 6-1 | 205 | R | R | AAA | | College of San Mateo |
| 17 | 513 | June-Reg | Marcus Sanders | | SS | 17 | 8/25/1985 | 6-0 | 170 | R | R | A+ | | Sarasota High School (Sarasota,FL) |
| 18 | 543 | June-Reg | Patrick Dobson | | OF | 22 | 12/8/1980 | 6-3 | 210 | R | R | AA | | UNLV |
| 19 | 573 | June-Reg | Jon Coutlangus | | OF | 22 | 10/21/1980 | 6-1 | 180 | L | L | MLB | 2007-2007 | University of South Carolina |
| 20 | 603 | June-Reg | Raul Rodriguez | | C | 18 | 7/27/1984 | 6-0 | 195 | R | R | - | | Florida Christian High School (Miami,FL) |
| 21 | 633 | June-Reg | Sean Watson | | P | 17 | 7/24/1985 | 6-3 | 215 | R | R | AA | | Florida Christian High School (Miami,FL) |
| 22 | 663** | June-Reg | Nate Fogle | | P | 19 | 12/27/1983 | 6-4 | 205 | R | R | A+ | | Mount Hood Community College |
| 23 | 693 | June-Reg | Mike Kunes | | P | 21 | 9/16/1981 | 6-2 | 210 | L | L | A- | | UCLA |
| 24 | 723 | June-Reg | Brian Wilson | | P | 21 | 3/16/1982 | 6-1 | 205 | R | R | MLB | 2006-2008 | Louisiana State University |
| 25 | 753** | June-Reg | Nolan Mulligan | | P | 18 | 1/30/1985 | 6-5 | 190 | R | R | Rookie | | Chaminade-Madonna High School (Hollywood,FL) |
| 26 | 783 | June-Reg | Tyler Coon | | P | 19 | 11/1/1983 | 6-3 | 210 | L | L | College | | Community College of Southern Nevada |
| 27 | 813** | June-Reg | Omar Aguilar | | P | 18 | 3/31/1985 | 6-1 | 190 | L | R | AA | | Livingston High School (Livingston,CA) |
| 28 | 843 | June-Reg | Tony Gonzalez | | OF | 19 | 4/22/1984 | 6-5 | 212 | R | R | College | | Sunny Hills High School (Fullerton,CA) |
| 29 | 873 | June-Reg | Daniel DeSouza | | OF | 18 | 11/27/1984 | 6-1 | 175 | L | L | Rookie | | Connors State College |
| 30 | 903 | June-Reg | Derek Barrows | | 3B | 22 | 11/20/1980 | 6-1 | 187 | R | R | A | | Campbell University |
| 31 | 933 | June-Reg | Eduardo Baez | | P | 18 | 10/19/1984 | 6-0 | 172 | R | R | - | | Mission College |
| 32 | 963** | June-Reg | O.D. Gonzalez | | OF | 18 | 9/12/1984 | 6-1 | 180 | R | R | A | | American High School (Hialeah,FL) |
| 33 | 993 | June-Reg | Travis NeSmith | | P | 21 | 4/26/1982 | 6-3 | 225 | L | L | A | | Florida Atlantic University |
| 34 | 1023 | June-Reg | Cody McAllister | | P | 19 | 3/21/1984 | 6-2 | 190 | R | R | A+ | | Edmonds Community College |
| 35 | 1053** | June-Reg | Tyson Brummett | | P | 18 | 8/15/1984 | 6-2 | 180 | R | R | A+ | | Spanish Fork High School (Spanish Fork,UT) |
| 36 | 1083 | June-Reg | Tim Alvarez | | P | 22 | 1/5/1981 | 6-4 | 235 | L | L | A+ | | Southeast Missouri State University |
| 37 | 1113** | June-Reg | Shannon Wirth | | P | 19 | 5/27/1984 | 6-1 | 195 | R | R | A+ | | Mount Hood Community College |
| 38 | 1143 | June-Reg | Jordan Hafer | | 1B | 18 | 11/22/1984 | 6-2 | 200 | B | L | College | | Deerfield Beach High School (Deerfield Beach,FL) |
| 39 | 1173 | June-Reg | Mike Pierce | | C | 19 | 4/19/1984 | 6-3 | 185 | R | R | - | | Fresno City College |
| 40 | 1203 | June-Reg | Dylan Gonzalez | | P | 18 | 3/7/1985 | 6-3 | 175 | R | R | A | | American Heritage High School (Plantation,FL) |
| 41 | 1232 | June-Reg | Mike Johnston | | P | 21 | 10/10/1981 | 6-2 | 190 | L | L | College | | Ball State University |
| 42 | 1261** | June-Reg | Luis Martinez | | C | 18 | 4/3/1985 | 6-0 | 210 | R | R | A | | Coral Park High School (Miami,FL) |
| 43 | 1289** | June-Reg | Mike Bell | | C | 18 | 3/30/1985 | 5-11 | 175 | R | R | AA | | Red Bluff High School (Red Bluff,CA) |
| 44 | 1317 | June-Reg | John Odom | | P | 21 | 1/6/1982 | 6-2 | 185 | R | R | A | | Tallahassee Community College |
| 45 | 1344 | June-Reg | James Braden | | P | 19 | 3/10/1984 | 6-1 | 175 | R | R | - | | Manatee Community College |
| 46 | 1371 | June-Reg | Brandon Federici | | P | 18 | 8/10/1984 | 200 | | L | L | - | | Polk Community College |
| 47 | 1398 | June-Reg | Thomas Correa | | SS | 17 | 10/20/1985 | 5-8 | 165 | R | R | - | | Florin High School (Sacramento,CA) |
| 48 | 1425 | June-Reg | Matt Berezay | | OF | 19 | 11/15/1983 | 5-11 | 190 | B | R | AA | | Modesto Junior College |
| 49 | 1451** | June-Reg | Doug Fister | | P | 19 | 2/4/1984 | 6-8 | 185 | L | R | AA | | Merced College |
| 50 | 1477 | June-Reg | Jim Popp | | P | 22 | 1/29/1981 | 6-4 | 190 | R | R | Ind | | Duquesne University |
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