| 1 | 21 | June-Reg | Alvie Shepherd | P | 21 | 6-7 | 220 | R | R | AA | | University of Nebraska | $650,000 |
| 2 | 51 | June-Reg | Chip Alley | OF | 18 | 6-3 | 190 | B | R | AA | | Palm Beach Lakes (West Palm Beach,FL) | $325,000 |
| 3 | 80 | June-Reg | Darrell Dent | OF | 18 | 6-2 | 175 | L | L | AAA | | Montclair Prep (Van Nuys,CA) | |
| 4 | 108 | June-Reg | Louis Fisher | P | 18 | 6-1 | 189 | R | R | AA | | Fremont (Oakland,CA) | |
| 5 | 136** | June-Reg | Luke Hudson | P | 18 | 6-3 | 195 | R | R | MLB | 2002-2007 | Fountain Valley (Fountain Valley,CA) | |
| 6 | 164** | June-Reg | John Bale | P | 21 | 6-4 | 220 | L | L | MLB | 1999-2009 | University of Southern Mississippi | |
| 7 | 192 | June-Reg | Kevin Miller | 3B | | | | | | - | | Ballard (Seattle,WA) | |
| 8 | 220 | June-Reg | Scott Eibey | P | 21 | 6-4 | 208 | L | L | AA | | University of Northern Iowa | |
| 9 | 248 | June-Reg | Joel Stephens | OF | 19 | 6-1 | 207 | R | R | A | | Notre Dame (Elmira,NY) | |
| 10 | 276 | June-Reg | David Dellucci | OF | 21 | 5-10 | 180 | L | L | MLB | 1997-2009 | University of Mississippi | |
| 11 | 304 | June-Reg | Greg Dean | P | 21 | 6-2 | 220 | R | R | AA | | Oklahoma State University | |
| 12 | 332 | June-Reg | Carlos Akins | OF | 20 | 6-0 | 180 | R | R | A+ | | Western Kentucky University | |
| 13 | 360 | June-Reg | Bob O'Toole | OF | 21 | 6-0 | 195 | R | R | AA | | Providence College | |
| 14 | 388 | June-Reg | Chris Bryant | 3B | 22 | 6-2 | 195 | R | R | A+ | | North Carolina Wesleyan College | |
| 15 | 416 | June-Reg | Tim Olszewski | p | 21 | 6-2 | 200 | R | R | A+ | | Triton College | |
| 16 | 444** | June-Reg | Zach Sorensen | SS | 18 | 6-0 | 190 | B | R | MLB | 2003-2005 | Highland (Salt Lake City,UT) | |
| 17 | 472 | June-Reg | Jason Lecronier | OF | 22 | 6-0 | 180 | L | R | AA | | McNeese State University | |
| 18 | 500** | June-Reg | Lawrence Adams | 1B | 18 | 6-5 | 215 | R | R | A- | | Creekside (Fairburn,GA) | |
| 19 | 528 | June-Reg | Brion King | OF | 18 | 6-0 | 200 | R | R | A+ | | Oviedo (Oviedo,FL) | |
| 20 | 556 | June-Reg | Carlos Casillas | 1B | | | | | | - | | Santa Monica (Santa Monica,CA) | |
| 21 | 584 | June-Reg | Dan Reed | p | 20 | 6-4 | 210 | R | L | A+ | | Stanford University | |
| 22 | 612** | June-Reg | Doug Thompson | p | 18 | 6-1 | 195 | R | R | AAA | | Mississippi Gulf Coast Community College | |
| 23 | 640 | June-Reg | Matt Achilles | p | 16 | 6-3 | 190 | R | R | AA | | Black Hawk College | |
| 24 | 668 | June-Reg | Jason Albert | 2B | | | | | | - | | Central Connecticut State University | |
| 25 | 696 | June-Reg | Gaylon Dixon | p | | | | | | - | | Seminole Community College | |
| 26 | 724 | June-Reg | Joaquin Serra | SS | 19 | 5-9 | 164 | R | R | Rookie | | | |
| 27 | 752 | June-Reg | Robert Morseman | p | 21 | 6-4 | 190 | L | L | A+ | | Salem International University | |
| 28 | 780 | June-Reg | Johnny Isom | OF | 21 | 5-11 | 210 | R | R | AAA | | Texas Wesleyan University | |
| 29 | 808 | June-Reg | Tom Russin | 1B | 21 | 6-2 | 200 | R | R | A+ | | Eckerd College | |
| 30 | 836 | June-Reg | Chris Bray | p | 20 | 6-4 | 200 | R | R | A+ | | Mount Olive College | |
| 31 | 864 | June-Reg | A.J. Marguardt | OF | | | | | | - | | Columbia Basin College | |
| 32 | 892 | June-Reg | William Morstad | 3B | | | | | | - | | Windsor Academy (Macon,GA) | |
| 33 | 920** | June-Reg | Mike Cosgrove | p | 19 | 6-2 | 195 | R | R | AAA | | Cypress College | |
| 34 | 948** | June-Reg | Darin Moore | p | 18 | 6-0 | 195 | R | R | AA | | Lodi (Lodi,CA) | |
| 35 | 976 | June-Reg | Calvin Pickering | Of-1B | 18 | 6-5 | 278 | L | L | MLB | 1998-2005 | King (Tampa,FL) | |
| 36 | 1004** | June-Reg | John Santos | p | | | | | | - | | Corcoran (Corcoran,CA) | |
| 37 | 1032 | June-Reg | Avery Taylor | SS | 19 | 6-0 | 202 | R | R | Rookie | | Long Beach (Long Beach,MS) | |
| 38 | 1060 | June-Reg | Ken Sims | p | 19 | 6-4 | 215 | R | R | AA | | New Mexico Junior College | |
| 39 | 1088 | June-Reg | Craig Jones | p | 18 | 6-2 | 190 | R | R | A- | | La Quinta (Westminster,CA) | |
| 40 | 1116 | June-Reg | Cory Scott | p | | | | | | Ind | | Currituck County (Barco,NC) | |
| 41 | 1144** | June-Reg | Josh Taylor | SS | | | | | | - | | Shawnee (Shawnee,OK) | |
| 42 | 1172** | June-Reg | Jerry Hairston | 2B | 19 | 5-10 | 173 | R | R | MLB | 1998-2009 | Naperville North (Naperville,IL) | $0 |
| 43 | 1200** | June-Reg | Jason Glover | of | 21 | 6-0 | 195 | R | R | Rookie | | Georgia College & State University | |
| 44 | 1228 | June-Reg | Mike Wooden | p | | | | | | - | | North County Tech (Linthicum,MD) | |
| 45 | 1254 | June-Reg | Chris Paxton | C | 18 | 6-2 | 210 | L | R | AA | | Palmdale (Palmdale,CA) | |
| 46 | 1278 | June-Reg | Dan Keller | p | | | | | | - | | Fountain Valley (Fountain Valley,CA) | |
| 47 | 1302 | June-Reg | Corey Coll | p | | | | | | - | | Key (Union Bridge,MD) | |
| 48 | 1324 | June-Reg | Wess Winn | SS | 23 | 5-10 | 175 | B | R | Rookie | | University of Texas-Arlington | |
| 49 | 1346 | June-Reg | Robert Williams | C | | | | | | - | | Edgewater (Orlando,FL) | |