| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 11 | June-Reg | Kenny Baugh | $$ | P | 22 | 2/5/1979 | 6-4 | 190 | R | R | AAA | | Rice University |
| 1 | 32 | June-Reg | Mike Woods | $$ | IF | 20 | 9/11/1980 | 6-1 | 200 | R | R | AA | | Southern University |
| 2 | 55 | June-Reg | Preston Larrison | $$ | P | 20 | 11/19/1980 | 6-4 | 215 | R | R | AAA | | University of Evansville |
| 2 | 65 | June-Reg | Matt Coenen | $$ | P | 21 | 3/13/1980 | 6-6 | 230 | L | L | AA | | Charleston Southern University |
| 3 | 87 | June-Reg | Jack Hannahan | $$ | 3B | 21 | 3/4/1980 | 6-2 | 200 | L | R | MLB | 2006-2007 | University of Minnesota |
| 4 | 117 | June-Reg | Mike Rabelo | | C | 21 | 1/17/1980 | 6-1 | 200 | B | R | MLB | 2006-2007 | University of Tampa |
| 5 | 147 | June-Reg | Ryan Raburn | | 3B | 20 | 4/17/1981 | 6-0 | 180 | R | R | MLB | 2004-2007 | South Florida Community College |
| 6 | 177 | June-Reg | Jason Knoedler | | OF | 20 | 7/17/1980 | 6-1 | 190 | B | R | AA | | University of Miami (Florida) |
| 7 | 207 | June-Reg | Tom Farmer | | P | 21 | 7/27/1979 | 6-2 | 195 | R | R | AAA | | University of Miami (Florida) |
| 8 | 237 | June-Reg | Donald Kelly | | SS | 21 | 2/15/1980 | 6-4 | 190 | L | R | MLB | 2007-2007 | Point Park College (Pa.) |
| 9 | 267 | June-Reg | David Mattle | | OF | 21 | 12/21/1979 | 6-0 | 200 | L | R | A+ | | Kent State University |
| 10 | 297 | June-Reg | Vincent Blue | | OF | 18 | 2/8/1983 | 6-2 | 180 | L | R | AAA | | Lamar High School (Houston,TX) |
| 11 | 327** | June-Reg | Eric Thomas | | P | 20 | 3/24/1981 | 6-7 | 246 | R | R | A+ | | Briarcliffe College |
| 12 | 357 | June-Reg | James Gonzales | | P | 21 | 8/4/1979 | 6-1 | 185 | R | R | College | | University of California-Santa Barbara |
| 13 | 387 | June-Reg | Landon Stockman | | P | 21 | 8/28/1979 | 6-2 | 190 | R | R | A+ | | Kennesaw State University |
| 14 | 421 | June-Reg | Matt Williams | | OF | 17 | 11/18/1983 | 6-2 | 170 | B | R | A- | | Fontana High School (Fontana,CA) |
| 15 | 447 | June-Reg | Kevin McDowell | | P | 22 | 11/20/1978 | 6-2 | 200 | L | L | AA | | Bucknell University |
| 16 | 477** | June-Reg | Joey Metropoulos | | 3B | 17 | 10/7/1983 | 6-1 | 230 | R | R | A | | Monte Vista High School (Spring Valley,CA) |
| 17 | 507 | June-Reg | Dan Smith | | P | 22 | 11/29/1978 | 6-4 | 215 | R | R | A+ | | University of Miami (Florida) |
| 18 | 537 | June-Reg | Alex Trezza | | C-1B | 20 | 9/1/1980 | 6-3 | 210 | L | R | A+ | | Stony Brook University |
| 19 | 567 | June-Reg | William Ryan | | 3B | 19 | 7/21/1981 | 6-3 | 200 | R | R | A- | | Briarcliffe College |
| 20 | 597 | June-Reg | Jason Moates | | P | 22 | 8/22/1978 | 6-2 | 210 | R | R | A+ | | Middle Tennessee State University |
| 21 | 627** | June-Reg | Tim Dorn | | P | 18 | 12/30/1982 | 6-8 | 245 | R | R | A | | Monrovia High School (Monrovia,CA) |
| 22 | 657 | June-Reg | Francisco Rosado | | OF | 19 | 11/27/1981 | 5-10 | 230 | R | R | Rookie | | Antelope Valley College |
| 23 | 687 | June-Reg | Mike Scott | | OF | 22 | 11/17/1978 | 5-10 | 175 | L | L | A | | University of Connecticut |
| 24 | 717** | June-Reg | John Schneider | | C | 21 | 2/14/1980 | 6-3 | 215 | R | R | AAA | | University of Delaware |
| 25 | 747 | June-Reg | Chris Kolodzey | | OF | 21 | 7/15/1979 | 6-0 | 200 | R | R | A | | University of Delaware |
| 26 | 777 | June-Reg | Herman Dean | | OF | 20 | 11/25/1980 | 6-3 | 190 | R | R | A- | | Citrus Junior College |
| 27 | 807 | June-Reg | Mike Kobow | | P | 22 | 4/9/1979 | 6-4 | 190 | R | R | AA | | University of Minnesota |
| 28 | 837 | June-Reg | Jon Connolly | | P | 17 | 8/24/1983 | 6-0 | 205 | R | L | AAA | | Oneonta High School (Oneonta,NY) |
| 29 | 867 | June-Reg | Garth McKinney | | OF | 19 | 5/7/1982 | 6-3 | 210 | R | R | AA | | Walters State Community College |
| 30 | 897 | June-Reg | John Birtwell | | P | 21 | 9/4/1979 | 6-2 | 225 | R | R | AAA | | Harvard University |
| 31 | 927 | June-Reg | Humberto Sanchez | | P | 18 | 5/28/1983 | 6-6 | 230 | R | R | AAA | | Rockland Community College |
| 32 | 957 | June-Reg | Trevor Leu | | P | 22 | 12/29/1978 | 6-2 | 200 | L | L | A+ | | Oral Roberts University |
| 33 | 987 | June-Reg | Michael Howell | | P | 21 | 11/9/1979 | 6-4 | 200 | R | R | A+ | | Binghamton University |
| 34 | 1017 | June-Reg | Ian Ostlund | | P | 22 | 10/17/1978 | 6-1 | 200 | R | L | AAA | | Virginia Tech |
| 35 | 1047 | June-Reg | Charles Lombardy | | P | 22 | 9/20/1978 | 6-2 | 210 | L | R | - | | Ohio University |
| 36 | 1077 | June-Reg | Jed Stringham | | OF | 23 | 12/28/1977 | 6-3 | 210 | R | R | A | | University of California-Santa Barbara |
| 37 | 1107 | June-Reg | Kevin Miller | | | | | | | | | College | | Cuesta College |
| 38 | 1137** | June-Reg | Adam Harben | | P | 17 | 8/19/1983 | 6-5 | 210 | R | R | AA | | Central Arkansas Christian High School (North Little Rock,AR) |
| 39 | 1167 | June-Reg | Robert White | | | | | | | | | College | | Spartanburg Methodist College |
| 40 | 1197 | June-Reg | Tom Lyons | | P | 18 | 3/22/1983 | 6-2 | 200 | R | R | A- | | Downers Grove North High School (Downers Grove,IL) |
| 41 | 1226 | June-Reg | Trey Holloway | | P | 18 | 8/24/1982 | 6-1 | 190 | R | L | College | | Booneville High School (Booneville,AR) |
| 42 | 1255 | June-Reg | Coby Judd | | P | | | | 0 | | | - | | Simi Valley High School (Simi Valley,CA) |
| 43 | 1283** | June-Reg | Sean Richardson | | C | | | | 0 | | | - | | Vista High School (Vista,CA) |
| 44 | 1311** | June-Reg | Phil Sobkow | | P | 20 | 6/17/1981 | 6-5 | 220 | B | R | A | | Butte Community College |
| 45 | 1339 | June-Reg | Brent Hale | | P | 19 | 5/14/1982 | 6-2 | 200 | R | R | College | | Palos Verdes Peninsula High School (Rollings Hills Estates,CA) |
| 46 | 1367 | June-Reg | Lonnie Patterson | | P | | | | 0 | | | - | | Harlan High School (Chicago,IL) |
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