| 1 | 16 | June-Reg | Joe Fontenot | P | 18 | 6-2 | 185 | R | R | MLB | 1998-1998 | Acadiana (Lafayette,LA) | $900,000 |
| 2 | 46 | June-Reg | Jason Brester | P | 18 | 6-3 | 190 | L | L | AA | | | $292,500 |
| 3 | 75 | June-Reg | Darin Blood | P | 20 | 6-2 | 180 | R | R | AAA | | Gonzaga University | |
| 4 | 103 | June-Reg | Russ Ortiz | P | 21 | 6-1 | 210 | R | R | MLB | 1998-2009 | University of Oklahoma | |
| 5 | 131 | June-Reg | Jim Woodrow | P | 22 | 6-6 | 240 | R | R | A- | | Flagler College | |
| 6 | 159 | June-Reg | Joe Nathan | P | 20 | 6-4 | 205 | R | R | MLB | 1999-2009 | Stony Brook University | |
| 7 | 187 | June-Reg | Alex Morales | OF | | | | | | A+ | | University of Central Florida | |
| 8 | 215 | June-Reg | Ben Tucker | P | 21 | 6-4 | 210 | R | R | AA | | USC | |
| 9 | 243 | June-Reg | Manny Bermudez | P | 18 | 6-1 | 190 | R | R | AA | | | |
| 10 | 271 | June-Reg | Jeff Hutzler | P | 22 | 6-6 | 225 | R | R | AA | | University of Texas-San Antonio | |
| 11 | 299 | June-Reg | Ian Rand | OF | 18 | 6-4 | 190 | R | R | A+ | | Helix Charter (La Mesa,CA) | |
| 12 | 327 | June-Reg | Bruce Thompson | OF | | | | | | A | | University of Miami | |
| 13 | 355 | June-Reg | Philip Bailey | p | 21 | 6-1 | 190 | L | L | A+ | | University of Central Arkansas | |
| 14 | 383 | June-Reg | Jon Watson | 2B | | | | | | A+ | | Fairleigh Dickinson University | |
| 15 | 411** | June-Reg | Nathan Forbush | C-1B | 19 | 6-2 | 220 | B | R | A+ | | Central Arizona College | |
| 16 | 439 | June-Reg | Brian Knoll | p | 21 | 6-3 | 200 | R | R | AAA | | Brigham Young University | |
| 17 | 467** | June-Reg | Duane Eason | p | | | | | | - | | Brookdale Community College | |
| 18 | 495 | June-Reg | Rogelio Colon | p | | | | | | - | | | |
| 19 | 523 | June-Reg | Kurt Takahashi | p | 21 | 6-4 | 215 | R | R | A+ | | Fresno City College | |
| 20 | 551 | June-Reg | Andy Norton | C | | | | | | A- | | Gonzaga University | |
| 21 | 579 | June-Reg | Terry Weaver | SS | | | | | | AA | | Liberty University | |
| 22 | 607 | June-Reg | Danny Harmon | p | | | | | | - | | Midland (Pleasant Plains,AR) | |
| 23 | 635 | June-Reg | Mark Peer | OF | | | | | | - | | St. Louis Community College-Meramec | |
| 24 | 663** | June-Reg | Toby Hall | C | 19 | 6-3 | 205 | R | R | MLB | 2000-2008 | American River College | |
| 25 | 691 | June-Reg | Marc Mosman | p | | | | | | A | | Cal State Dominguez Hills | |
| 26 | 719 | June-Reg | Jeff Pohl | p | 19 | 6-4 | 215 | R | R | A- | | Three Rivers Community College | |
| 27 | 747** | June-Reg | Billy Coleman | p | | | | | | - | | Davidson (Davidson,OK) | |
| 28 | 775 | June-Reg | Jeremy Jackson | OF | | | | | | - | | Indian Hills Community College-Centerville | |
| 29 | 803 | June-Reg | Kelly Ireland | OF | | | | | | - | | Mount Hood Community College | |
| 30 | 831 | June-Reg | John McMurray | 3B | | | | | | - | | Monticello (Monticello,AR) | |
| 31 | 859 | June-Reg | Shawn Lindsay | OF | | | | | | - | | Franklin (Portland,OR) | |
| 32 | 887 | June-Reg | Brian Phelan | C | | | | | | - | | Denver East (Denver,CO) | |
| 33 | 915** | June-Reg | Brian Little | 3B | | | | | | - | | Tulare Union (Tulare,CA) | |
| 34 | 943** | June-Reg | Justin Miller | p | 17 | 6-2 | 195 | R | R | MLB | 2002-2009 | Torrance (Torrance,CA) | |
| 35 | 971** | June-Reg | Matthew Schuldt | C | 19 | 6-2 | 205 | R | R | A+ | | Howard College | |
| 36 | 999 | June-Reg | Brandon Hayes | p | | | | | | - | | McLane (Fresno,CA) | |
| 37 | 1027** | June-Reg | Jason Dewey | C | 18 | 6-1 | 190 | R | R | AAA | | | |
| 38 | 1055 | June-Reg | LaJuan Rice | Of | | | | | | - | | McNair (Atlanta,GA) | |
| 39 | 1083 | June-Reg | Tom Topaum | C | | | | | | A- | | Centennial (Gresham,OR) | |
| 40 | 1111 | June-Reg | Mike Lincoln | p | 20 | 6-2 | 211 | R | R | MLB | 1999-2009 | American River College | |
| 41 | 1139 | June-Reg | Mike Littlefield | p | | | | | | - | | Central Arizona College | |
| 42 | 1167** | June-Reg | Brad Lidge | p | 18 | 6-5 | 200 | R | R | MLB | 2002-2009 | Cherry Creek (Englewood,CO) | |
| 43 | 1195** | June-Reg | Jason Huth | SS | 18 | 5-11 | 180 | B | R | A | | Cherry Creek (Englewood,CO) | |
| 44 | 1223** | June-Reg | Mike Davis | p | 19 | 5-11 | 180 | R | R | A- | | Tallahassee Community College | |
| 45 | 1249** | June-Reg | Eric Thompson | p | 17 | 6-2 | 190 | R | R | AAA | | Greenon (Springfield,OH) | |
| 46 | 1273** | June-Reg | Casey Bookout | 1B | 18 | 6-5 | 225 | L | R | A | | Stroud (Stroud,OK) | |
| 47 | 1297 | June-Reg | Joe Blasingim | p | 22 | 6-4 | 190 | R | R | A | | Missouri State University | |
| 48 | 1319 | June-Reg | Kirk Boiling | p | | | | | | - | | West Torrance (Torrance,CA) | |
| 49 | 1341** | June-Reg | Dave Townsend | p | 20 | 6-2 | 225 | R | R | AA | | Delta State University | |
| 50 | 1363 | June-Reg | Edwards Guzman | 3B | 18 | 5-10 | 205 | L | R | MLB | 1999-2003 | | |