| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 13 | June-Reg | Shaun Boyd | $$ | IF | 18 | 8/15/1981 | 5-10 | 175 | R | R | AAA | - | Vista High School (Vista,CA) |
| 1 | 24 | June-Reg | Blake Williams | $$ | P | 21 | 2/22/1979 | 6-5 | 225 | R | R | A+ | | Southwest Texas State University |
| 2 | 53 | June-Reg | Chris Narveson | | P | 18 | 12/20/1981 | 6-3 | 180 | L | L | MLB | 2006-2006 | T.C. Roberson High School (Asheville,NC) |
| 3 | 83 | June-Reg | Chase Voshell | | IF | 21 | 3/29/1979 | 6-2 | 185 | R | R | A+ | | Wake Forest University |
| 4 | 113 | June-Reg | Yadier Molina | | C | 17 | 7/13/1982 | 5-11 | 187 | R | R | MLB | 2004-2008 | Maestro Ladi High School (Vega Alta,PR) |
| 5 | 143 | June-Reg | Josh Axelson | | P | 21 | 12/4/1978 | 6-1 | 201 | R | R | AA | | Michigan State University |
| 6 | 173 | June-Reg | Justin Woodrow | | LF | 18 | 3/26/1982 | 6-2 | 195 | L | R | A- | | Knoch High School (Saxonburg,PA) |
| 7 | 203 | June-Reg | Shaun Stokes | | P | 21 | 8/23/1978 | 6-2 | 210 | R | R | A | | William Paterson University of New Jersey |
| 8 | 233 | June-Reg | Dan Moylan | | C | 21 | 4/24/1979 | 6-0 | 190 | L | R | AAA | | University of North Carolina |
| 9 | 263 | June-Reg | John Novinsky | | P | 21 | 4/25/1979 | 6-3 | 180 | R | R | AAA | | Iona College |
| 10 | 293 | June-Reg | Carmen Cali | | P | 21 | 11/4/1978 | 5-10 | 185 | L | L | MLB | 2004-2007 | Florida Atlantic University |
| 11 | 323 | June-Reg | John Gall | | 1B | 22 | 4/2/1978 | 6-0 | 195 | R | R | MLB | 2005-2007 | Stanford University |
| 12 | 353 | June-Reg | Roddy Friar | | C | 24 | 5/10/1976 | 6-0 | 190 | R | R | A+ | | University of Southern Colorado |
| 13 | 383 | June-Reg | Matt Galante | | 2B | 21 | 10/10/1978 | 5-8 | 160 | R | R | A+ | | St. John's University |
| 14 | 413 | June-Reg | Dee Haynes | | LF | 22 | 2/22/1978 | 6-0 | 205 | R | R | AAA | | Delta State University |
| 15 | 443 | June-Reg | Chris Morris | | CF | 20 | 7/1/1979 | 5-8 | 180 | B | R | AA | | The Citadel |
| 16 | 473 | June-Reg | Jutt Hileman | | OF | 18 | 7/13/1981 | 6-1 | 185 | R | R | A+ | | Palmyra High School (Palmyra,PA) |
| 17 | 503** | June-Reg | Kaulana Kuhaulua | | IF | 20 | 1/30/1980 | 6-0 | 166 | R | R | AA | | Los Angeles Community College |
| 18 | 533** | June-Reg | Marc LaMacchia | | P | 18 | 3/27/1982 | 6-0 | 195 | R | R | AA | | East Lake High School (Tarpon Springs,FL) |
| 19 | 563 | June-Reg | Chet Medlock | | P | 21 | 10/23/1978 | 6-1 | 170 | R | R | A+ | | McNeese State University |
| 20 | 593 | June-Reg | Landon Brandes | | 3B | 21 | 3/15/1979 | 6-1 | 185 | R | R | A+ | | University of Missouri |
| 21 | 623 | June-Reg | Bryan Schultz | | P | 22 | 12/27/1977 | 6-1 | 180 | R | R | A | | University of Nevada |
| 22 | 653 | June-Reg | Billy Schmitt | | 1B | 17 | 8/16/1982 | 6-1 | 205 | R | R | A- | | Green Valley High School (Henderson,NV) |
| 23 | 683 | June-Reg | Mike Meyer | | P | 22 | 12/18/1977 | 6-2 | 180 | R | R | A+ | | University of Arizona |
| 24 | 713 | June-Reg | John Lockhart | | P | 21 | 8/21/1978 | 6-1 | 195 | R | R | Rookie | | Centenary College |
| 25 | 743 | June-Reg | Ryan Hamill | | C | 21 | 10/3/1978 | 6-0 | 200 | R | R | A+ | | UCLA |
| 26 | 773 | June-Reg | Matt Dogero | | C | 19 | 7/3/1980 | 6-0 | 210 | R | R | A | | Santa Barbara City College |
| 27 | 803** | June-Reg | Derek Roper | | P | 19 | 12/31/1980 | 6-6 | 200 | R | R | A | | Hutchinson Community College |
| 28 | 833 | June-Reg | Bryan Grassing | | P | 22 | 1/12/1978 | 6-0 | 220 | R | R | A+ | | Saint Leo University |
| 29 | 863 | June-Reg | David Lindsey | | P | 21 | 8/9/1978 | 6-4 | 225 | R | R | Rookie | | Loyola (NO) |
| 30 | 893** | June-Reg | Mailon Kent | | OF | 21 | 9/2/1978 | 6-3 | 215 | R | R | A+ | | Auburn University |
| 31 | 923 | June-Reg | Dan Firlit | | SS | 21 | 11/22/1978 | 6-1 | 195 | R | R | AA | | Southwest Missouri State University |
| 32 | 953 | June-Reg | Dallas Pallaro | | 2B | | | | 0 | | | - | | Dixie State College of Utah |
| 33 | 983 | June-Reg | Richie Burgess | | P | 20 | 10/9/1979 | 6-4 | 210 | R | R | A+ | | San Bernardino Valley College |
| 34 | 1013 | June-Reg | Tyler Johnson | | P | 19 | 6/7/1981 | 6-2 | 180 | B | L | MLB | 2005-2007 | Moorpark College |
| 35 | 1043 | June-Reg | John Santor | | 1B | 18 | 11/16/1981 | 6-1 | 215 | B | R | A+ | | Highland High School (Palmdale,CA) |
| 36 | 1073 | June-Reg | Troy Grimmer | | P | | | | 0 | | | - | | Rex Putnam High School (Milwaukie,OR) |
| 37 | 1103 | June-Reg | Matt Vriesenga | | P | 22 | 8/28/1977 | 6-5 | 190 | R | R | A | | Western Michigan University |
| 38 | 1133 | June-Reg | Bruce Nelson | | C | 21 | 8/27/1978 | 6-0 | 180 | R | R | A- | | Rockhurst University |
| 39 | 1163 | June-Reg | Preston Harriman | | 3B | 20 | 9/28/1979 | 6-0 | 180 | R | R | Ind | | North Arkansas College |
| 40 | 1193 | June-Reg | Nathaniel Meza | | P | 22 | 4/22/1978 | 6-1 | 185 | R | R | A- | | Palomar College |
| 41 | 1222 | June-Reg | Brian Fatur | | CF | 21 | 6/5/1979 | 6-0 | 180 | R | R | A+ | | Moorpark College |
| 42 | 1251 | June-Reg | Ty Soto | | | | | | | | | College | | Centennial High School (Bakersfield,CA) |
| 43 | 1280 | June-Reg | Adam Pritchard | | | | | | | | | College | | Griffin High School (Griffin,GA) |
| 44 | 1307 | June-Reg | Chad Cummings | | | | | | | | | College | | Saddleback College |
| 45 | 1333 | June-Reg | Kelly Johnson | | p | 20 | 5/9/1980 | 6-1 | 220 | R | R | A | | Yavapai College |
| 46 | 1357** | June-Reg | Matt Pender | | P | 19 | 6/11/1981 | 6-5 | 210 | R | R | A+ | | Middle Georgia College |
| 47 | 1381 | June-Reg | Felipe Tetelboin | | | 18 | 12/2/1981 | 5-10 | 176 | R | R | College | | Grant High School (Van Nuys,CA) |
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