| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 19 | June-Reg | Sean Burnett | $$ | P | 17 | 9/17/1982 | 6-1 | 176 | L | L | MLB | 2004-2008 | Wellington Christian High School (Wellington,FL) |
| 2 | 59 | June-Reg | David Beigh | | P | 19 | 2/2/1981 | 6-5 | 245 | R | R | A | | Harrison High School (West Lafayette,IN) |
| 3 | 89 | June-Reg | Chris Young | | P | 21 | 5/25/1979 | 6-10 | 258 | R | R | MLB | 2004-2008 | Princeton University |
| 4 | 119** | June-Reg | Patrick Boyd | | OF | 21 | 9/7/1978 | 6-3 | 205 | B | R | AA | - | Clemson University |
| 5 | 149 | June-Reg | Jason Sharber | $$ | P | 18 | 2/24/1982 | 6-3 | 224 | R | R | A+ | | Oakland High School (Mufreesboro,TN) |
| 6 | 179 | June-Reg | Josh Shortslef | | P | 18 | 2/1/1982 | 6-4 | 230 | R | L | AA | | Hannibal High School (Hannibal,NY) |
| 7 | 209 | June-Reg | Cole Burzynski | | P | 18 | 9/3/1981 | 6-4 | 200 | R | R | Rookie | | Navasota High School (Navasota,TX) |
| 8 | 239 | June-Reg | Kurt Shafer | | P | 18 | 12/4/1981 | 6-4 | 190 | R | R | A+ | | Land O'Lakes High School (Land O'Lakes,FL) |
| 9 | 269 | June-Reg | Chris Bass | | IF | 18 | 10/18/1981 | 6-2 | 180 | R | R | AA | | Madison Consolidated High School (Madison,IN) |
| 10 | 299 | June-Reg | Brandon Chaves | | SS | 20 | 8/5/1979 | 6-3 | 175 | B | R | AA | | University of Hawaii-Hilo |
| 11 | 329** | June-Reg | Kyle Parcus | | P | 18 | 10/7/1981 | 6-3 | 190 | L | L | AA | | Rosebud-Lott High School (Travis,TX) |
| 12 | 359 | June-Reg | Tim Keyser | | P | 18 | 10/3/1981 | 6-5 | 200 | R | R | Rookie | | Boyd County High School (Ashland,KY) |
| 13 | 389 | June-Reg | Troy Veleber | | P | 21 | 6/7/1979 | 5-10 | 165 | B | R | A- | | Jacksonville University |
| 14 | 419 | June-Reg | Vic Buttler | | OF | 19 | 8/12/1980 | 6-0 | 169 | L | L | AAA | | El Camino College |
| 15 | 449 | June-Reg | Sean Smith | | OF | 17 | 8/24/1982 | 5-10 | 180 | R | R | AA | | Joliet Township High School (Joliet,IL) |
| 16 | 479 | June-Reg | David Baum | | P | 20 | 6/13/1980 | 6-2 | 200 | L | L | - | | Okaloosa-Walton College |
| 17 | 509** | June-Reg | Daylon Monette | | OF | 19 | 4/8/1981 | 6-3 | 210 | B | R | A | | Cypress College |
| 18 | 539 | June-Reg | Jon Pagan | | 1B | | | | 0 | | | A- | | El Camino College |
| 19 | 569 | June-Reg | Mike Connolly | | P | 18 | 6/2/1982 | 6-0 | 169 | L | L | AAA | | Oneonta High School (Oneonta,NY) |
| 20 | 599 | June-Reg | Jose Bautista | | 3B | 19 | 10/19/1980 | 6-0 | 180 | R | R | MLB | 2004-2008 | Chipola College |
| 21 | 629 | June-Reg | John Larson | | P | | | | 0 | | | - | | Eastern Illinois University |
| 22 | 659 | June-Reg | Shannon Cabell | | P | 21 | 4/7/1979 | 6-0 | 197 | L | L | A | | West Virginia State College |
| 23 | 689 | June-Reg | Joshua Higgins | | P | 21 | 4/16/1979 | 6-5 | 185 | R | R | A+ | | Master's College, The |
| 24 | 719 | June-Reg | Ryan Kanekeberg | | P | 18 | 9/2/1981 | 6-4 | 200 | R | R | - | | Kamiak High School (Mukilteo,WA) |
| 25 | 749 | June-Reg | Nate McLouth | | OF | 18 | 10/28/1981 | 5-11 | 174 | L | R | MLB | 2005-2008 | Whitehall High School (Whitehall,MI) |
| 26 | 779 | June-Reg | Ian Snell | | P | 18 | 10/30/1981 | 5-11 | 164 | R | R | MLB | 2004-2008 | Caesar Rodney High School (Camden,DE) |
| 27 | 809 | June-Reg | Alex Cruz | | IF | 19 | 4/9/1981 | 6-0 | 143 | R | R | A+ | | Pasco Comprehensive High School (Dade City,FL) |
| 28 | 839** | June-Reg | Brian Hall | | | 18 | 2/1/1982 | 6-0 | 190 | R | R | A- | | |
| 29 | 869** | June-Reg | Denver Kitch | | IF | 19 | 11/25/1980 | 6-2 | 180 | R | R | A | | Yukon High School (Yukon,OK) |
| 30 | 899 | June-Reg | Chris Gale | | | 18 | 2/5/1982 | 6-5 | 220 | R | R | Ind | | Oyster River High School (Durham,NH) |
| 31 | 929 | June-Reg | Jeremy Blaylock | | P | | | | 0 | | | - | | North Hall High School (Gainesville,GA) |
| 32 | 959 | June-Reg | Danny Mackey | | | 17 | 8/7/1982 | 6-2 | 215 | R | R | College | | McQuaid Jesuit High School (Rochester,NY) |
| 33 | 989 | June-Reg | Michael Cockrell | | IF | 18 | 7/25/1981 | 5-10 | 160 | R | R | AA | | Los Angeles Harbor Community College |
| 34 | 1019 | June-Reg | Mike Fortin | | P | 22 | 7/31/1977 | 6-5 | 205 | R | R | A- | | American International (American International) |
| 35 | 1049 | June-Reg | Victor Ramos | | C | 18 | 10/4/1981 | 6-3 | 193 | L | R | AA | | Cayey (PR) |
| 36 | 1079 | June-Reg | Tim Baker | | P | | | | 0 | | | - | | Captain Shreve High School (Shreveport,LA) |
| 37 | 1109 | June-Reg | Joe Mcbride | | | | | | | | | College | | El Cerrito High School (El Cerrito,CA) |
| 38 | 1139 | June-Reg | Kevin Lee | | P | 18 | 11/18/1981 | 6-4 | 200 | R | R | Ind | | North High School (Wheaton,IL) |
| 39 | 1169 | June-Reg | Tristan Johnson | | 1B | 18 | 3/1/1982 | 6-3 | 230 | R | L | Rookie | | Woonsocket High School (Woonsocket,RI) |
| 40 | 1198 | June-Reg | Adam Blair | | | | | | | | | College | | Okaloosa-Walton College |
| 41 | 1227 | June-Reg | Mike Collum | | IF | 18 | 7/16/1981 | 6-3 | 185 | R | R | A | | Indian River Community College |
| 42 | 1256** | June-Reg | Jasha Balcom | | OF | 17 | 7/7/1982 | 5-10 | 175 | L | R | A | | Dublin High School (Dublin,GA) |
| 43 | 1284 | June-Reg | Jason Wilson | | | | | | | | | College | | Eastern Oklahoma State Community College |
| 44 | 1311 | June-Reg | Landon Kersey | | P | | | | 0 | | | - | | Caruthersville High School (Caruthersville,MO) |
| 45 | 1337 | June-Reg | Garrett Greer | | | | | | | | | College | | Veterans Memorial High School (Peabody,MA) |
| 46 | 1361 | June-Reg | Seth Hill | | | 19 | 5/6/1981 | 6-4 | 225 | L | L | A+ | | Kishwaukee Community College |
| 47 | 1385 | June-Reg | Matt Lindenmeyer | | | | | | | | | College | | Butler County Community College |
| 48 | 1405 | June-Reg | Andrew Kasparek | | | 18 | 11/21/1981 | 6-2 | 215 | R | R | Ind | | Weimar High School (Weimar,TX) |
| 49 | 1425 | June-Reg | Marc Love | | CF | 20 | 2/16/1980 | 6-1 | 200 | L | L | Rookie | | Galveston College |
| 50 | 1445 | June-Reg | Joshua Shackleford | | P | | | | 0 | | | - | | South Grand Prairie High School (Grand Prairie,TX) |
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