| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 2 | 48 | June-Reg | Kelly Shoppach | $$ | C | 21 | 4/29/1980 | 6-0 | 215 | R | R | MLB | 2005-2007 | Baylor University |
| 2 | 61** | June-Reg | Matt Chico | $$ | P | 18 | 6/10/1983 | 5-11 | 190 | L | L | MLB | 2007-2007 | Fallbrook High School (Fallbrook,CA) |
| 3 | 93 | June-Reg | Jon Devries | $$ | C | 18 | 8/22/1982 | 6-3 | 200 | R | R | AA | | Irvine High School (Irvine,CA) |
| 4 | 123 | June-Reg | Stefan Bailie | | IF | 21 | 5/16/1980 | 6-0 | 215 | R | R | AA | | Washington State University |
| 5 | 153 | June-Reg | Eric West | | IF | 18 | 3/24/1983 | 6-1 | 160 | R | R | A | | Southside High School (Gadsden,AL) |
| 6 | 183** | June-Reg | Justin James | | P | 20 | 9/13/1980 | 6-3 | 215 | R | R | AAA | | Yukon High School (Yukon,OK) |
| 7 | 213 | June-Reg | Rolando Viera | | P | 27 | 8/1/1973 | 5-10 | 182 | L | L | AAA | | Cuba (Cuba) |
| 8 | 243 | June-Reg | Kevin Youkilis | | IF | 22 | 3/15/1979 | 6-1 | 220 | R | R | MLB | 2004-2007 | University of Cincinnati |
| 9 | 273 | June-Reg | Billy Simon | | P | 18 | 11/11/1982 | 6-6 | 220 | R | R | A | | Wellington High School (Wellington,FL) |
| 10 | 303** | June-Reg | Ben Crockett | | P | 21 | 12/19/1979 | 6-3 | 200 | R | R | AAA | | Harvard University |
| 11 | 333 | June-Reg | Shane Rhodes | | P | 21 | 1/19/1980 | 6-2 | 200 | L | L | A+ | | West Virginia University |
| 12 | 363 | June-Reg | Ryan Brunner | | OF | 22 | 1/20/1979 | 6-0 | 220 | L | L | A | | University of Northern Iowa |
| 13 | 393 | June-Reg | Alec Porzel | | SS | 22 | 1/14/1979 | 5-11 | 190 | R | R | A- | | University of Notre Dame |
| 14 | 423 | June-Reg | Chris Farley | | P | 18 | 2/24/1983 | 6-2 | 180 | R | R | AAA | | Marhar Regional High School (Orange,MA) |
| 15 | 453 | June-Reg | Ryan Carroll | | P | 22 | 3/28/1979 | 6-6 | 220 | R | R | Ind | | Mississippi State University |
| 16 | 483 | June-Reg | Antonio Gonzalez | | CF | 18 | 3/10/1983 | 6-0 | 180 | R | R | - | | Framingham High School (Framingham,MA) |
| 17 | 513 | June-Reg | Michael Grant | | P | 21 | 11/12/1979 | 6-1 | 190 | R | R | A- | | Danville Area Community College |
| 18 | 543 | June-Reg | Brian Lane | | P | 20 | 12/5/1980 | 6-3 | 220 | R | R | A- | | University of Richmond |
| 19 | 573** | June-Reg | Jeremy Brown | | C | 21 | 10/25/1979 | 5-10 | 210 | R | R | MLB | 2006-2006 | University of Alabama |
| 20 | 603 | June-Reg | Devoris Williams | | OF | 17 | 8/8/1983 | 5-10 | 180 | B | R | A- | | Greensboro High School (Greensboro,AL) |
| 21 | 633 | June-Reg | Charlie Weatherby | | P | 22 | 12/23/1978 | 6-0 | 200 | R | R | AAA | | University of North Carolina-Wilmington |
| 22 | 663 | June-Reg | Jed Rogers | | P | 22 | 12/15/1978 | 6-2 | 205 | R | R | A- | | Boston College |
| 23 | 693 | June-Reg | Pedro Suarez | | P | 17 | 10/22/1983 | 6-3 | 190 | R | R | Rookie | | Mount Miguel High School (Spring Valley,CA) |
| 24 | 723** | June-Reg | Jason Ramos | | SS | 18 | 8/9/1982 | 6-0 | 185 | B | R | AA | | Braddock High School (Miami,FL) |
| 25 | 753 | June-Reg | Kris Coffey | | OF | 22 | 4/27/1979 | 5-9 | 175 | R | R | A | | Dallas Baptist University |
| 26 | 783 | June-Reg | Kenneth Trapp | | P | | | | 0 | | | - | | Dallas Baptist University |
| 27 | 813 | June-Reg | Bryan Kent | | 3B | 23 | 6/27/1978 | 6-0 | 190 | R | R | A | | Southwest Texas State University |
| 28 | 843** | June-Reg | Steven Ponder | | P | 21 | 11/16/1979 | 6-0 | 200 | B | L | A- | | Texas A&M University |
| 29 | 873 | June-Reg | Mario Campos | | OF | 22 | 11/24/1978 | 6-6 | 235 | R | R | A- | | Trevecca Nazarene University (Tenn.) |
| 30 | 903 | June-Reg | Richard Sander | | P | 20 | 10/27/1980 | 6-2 | 235 | R | R | A- | | California State University, San Bernardino |
| 31 | 933 | June-Reg | Brett Rudrude | | P | 22 | 1/23/1979 | 6-3 | 195 | R | R | AA | | California State University, San Bernardino |
| 32 | 963 | June-Reg | Kyle Jackson | | P | 18 | 4/9/1983 | 6-3 | 180 | R | R | AA | | |
| 33 | 993 | June-Reg | Chris Honsa | | P | 17 | 8/13/1983 | 6-3 | 185 | R | R | A+ | | Corona del Sol High School (Tempe,AZ) |
| 34 | 1023 | June-Reg | Eron Brown | | 3B | 18 | 12/20/1982 | 6-3 | 190 | R | R | - | | Auburn High School (Auburn,AL) |
| 35 | 1053** | June-Reg | Koley Kolberg | | P | 18 | 11/26/1982 | 6-1 | 176 | R | R | A | | Coppell High School (Coppell,TX) |
| 36 | 1083 | June-Reg | Adam Sabari | | 1B | | | | 0 | | | - | | |
| 37 | 1113 | June-Reg | Emmanuel Lopez | | 1B | 18 | 3/14/1983 | 6-3 | 205 | R | R | - | | Globe High School (Globe,AZ) |
| 38 | 1143 | June-Reg | Jacob Almestica | | P | 19 | 6/4/1982 | 6-4 | 160 | R | R | - | | Medardo Carazo High School (Trujillo Alto,PR) |
| 39 | 1173 | June-Reg | Ricky Bauer | | | 18 | 3/1/1983 | 6-2 | 170 | R | R | A- | | Mid Pacific Institute High School (Honolulu,HI) |
| 40 | 1203** | June-Reg | Josh Bolen | | OF | 21 | 5/5/1980 | 6-3 | 225 | R | R | A- | | Illinois Central College |
| 41 | 1232** | June-Reg | Bart Braun | | P | 19 | 2/8/1982 | 5-10 | 175 | L | L | Ind | | Napa Valley Junior College. |
| 42 | 1260 | June-Reg | Tommie Major | | | 18 | 9/15/1982 | 6-0 | 190 | R | R | College | | Briarcliffe College |
| 43 | 1288** | June-Reg | Tanner Wootan | | 2B | 18 | 10/14/1982 | 6-1 | 190 | B | R | A- | | Mountain View High School (Mesa,AZ) |
| 44 | 1316 | June-Reg | Terrence Taylor | | | | | | | | | College | | Marin Community College. |
| 45 | 1344 | June-Reg | Brent Tarbett | | OF | 20 | 11/30/1980 | 6-2 | 220 | R | R | A+ | | Community College of Southern Nevada |
| 46 | 1372 | June-Reg | Chris Keeran | | CF | | | | 0 | | | - | | Eastlake High School (Chula Vista,CA) |
| 47 | 1399 | June-Reg | Donald Benson | | OF | 20 | 9/22/1980 | 5-11 | 195 | R | R | A- | | Mount San Antonio College |
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