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| | 1 | 2 | Adam Johnson | $$ | P | 20 | 7/12/1979 | 6-2 | 210 | R | R | MLB | 2001-2003 | California State University, Fullerton |
| | 1 | 31** | Aaron Heilman | | P | 21 | 11/12/1978 | 6-5 | 220 | R | R | MLB | 2003-2007 | University of Notre Dame |
| | 2 | 42** | Tagg Bozied | | 1B | 20 | 7/24/1979 | 6-3 | 210 | R | R | AAA | | University of San Francisco |
| | 2 | 54 | J.D. Durbin | | P | 18 | 2/24/1982 | 6-0 | 188 | R | R | MLB | 2004-2007 | Coronado High School (Scottsdale,AZ) |
| | 3 | 72 | Colby Miller | | P | 18 | 3/19/1982 | 6-2 | 184 | R | R | AA | | Weatherford High School (Weatherford,OK) |
| | 4 | 102 | Jason Miller | | P | 17 | 7/20/1982 | 6-1 | 202 | L | L | MLB | 2007-2007 | Sarasota High School (Sarasota,FL) |
| | 5 | 132 | Edgardo Lebron | | 3B-1B | 17 | 8/16/1982 | 6-1 | 170 | B | R | A | | Florencia Garcia (Las Piedras,PR) |
| | 6 | 162 | Ronnie Corona | | P | 21 | 1/27/1979 | 6-0 | 188 | R | R | AA | | California State University, Fullerton |
| | 7 | 192 | James Tomlin | | OF | 17 | 8/12/1982 | 6-1 | 176 | R | R | AA | | St. Bernard High School (Playa del Ray,CA) |
| | 8 | 222 | Henry Bonilla | | P | 21 | 8/16/1978 | 6-0 | 195 | R | R | AAA | | Tulane University |
| | 9 | 252 | Ken Holubec | | P | 21 | 9/1/1978 | 6-0 | 225 | L | L | A+ | | University of Louisiana-Lafayette |
| | 10 | 282 | Kelley Gulledge | | C | 21 | 1/25/1979 | 6-1 | 200 | R | R | AA | | University of Alabama |
| | 11 | 312 | Josh Rabe | | OF | 21 | 10/15/1978 | 6-2 | 210 | R | R | MLB | 2006-2007 | Quincy University |
| | 12 | 342 | Jason Kubel | | OF | 18 | 5/25/1982 | 5-11 | 193 | L | R | MLB | 2004-2007 | Highland High School (Palmdale,CA) |
| | 13 | 372** | Shane Boyd | | P | 17 | 9/18/1982 | | | | | College | | Henry Clay High School (Lexington,KY) |
| | 14 | 402 | Cory Agar | | 1B-C | 19 | 4/19/1981 | 5-10 | 212 | R | R | A | | |
| | 15 | 432 | Jeff Lincoln | | P | 22 | 4/30/1978 | 6-2 | 189 | R | R | A+ | | Western Kentucky University |
| | 16 | 462 | Daniel Decola | | C | 20 | 7/24/1979 | 6-1 | 202 | R | R | A | | Slippery Rock University of Pennsylvania |
| | 17 | 492** | Paul Maholm | | P | 18 | 6/25/1982 | 6-2 | 215 | L | L | MLB | 2005-2007 | Germantown High School (Germantown,TN) |
| | 18 | 522 | Andrew Persby | | P | 22 | 5/2/1978 | 6-4 | 247 | R | R | A+ | | University of Minnesota |
| | 19 | 552 | Bruce Dohrman | | OF | 19 | 5/31/1981 | 6-3 | 225 | L | R | Rookie | | Garrett High School (Garrett,IN) |
| | 20 | 582** | T.J. Prunty | | P | 18 | 7/5/1981 | 6-3 | 200 | R | R | A | | St Paul Academy Summit (Inner Grove Heights,MN) |
| | 21 | 612 | Mark Michael | | 3B | | | | 0 | | | - | | Gloucester Catholic High School (Gloucester,NJ) |
| | 22 | 642 | Brett Groves | | SS | 21 | 10/1/1978 | 6-0 | 185 | B | R | AA | | Florida State University |
| | 23 | 672 | Jered Goodwin | | | | | | | | | College | | Oviedo High School (Oviedo,FL) |
| | 24 | 702 | Sam Taylor | | | 17 | 11/6/1982 | 5-7 | 158 | B | R | AA | | Skyline High School (Oakland,CA) |
| | 25 | 732 | Joseph Hamer | | C | | | | 0 | | | - | | Newbury Park High School (Newbury Park,CA) |
| | 26 | 762 | Jeremy Fortner | | | | | | | | | College | | Venice High School (Venice,FL) |
| | 27 | 792** | Steve Reiss | | | 17 | 7/30/1982 | 6-5 | 190 | R | R | Rookie | | Vaughan High School (Thornhill,ON) |
| | 28 | 822** | Daniel Davidson | | P | 19 | 1/8/1981 | 6-4 | 225 | L | L | AAA | | Gulf Coast Community College |
| | 29 | 852 | Tom Sullivan | | P | 21 | 9/8/1978 | 5-10 | 170 | L | L | Rookie | | Slippery Rock University of Pennsylvania |
| | 30 | 882 | Shawn Cline | | C | 18 | 2/2/1982 | 6-1 | 215 | R | R | Rookie | | Baker County High School (MacClenny,FL) |
| | 31 | 912 | Beau Kemp | | P | 19 | 10/31/1980 | 6-0 | 188 | R | R | AAA | | Saddleback College |
| | 32 | 942 | Cody Kimball | | P | 18 | 12/14/1981 | 6-4 | 190 | R | R | Rookie | | MacArthur High School (Irving,TX) |
| | 33 | 972 | David Nowak | | CF | 19 | 6/29/1981 | 6-3 | 190 | L | L | Ind | | Arcadia High School (Phoenix,AZ) |
| | 34 | 1002 | Luke Martin | | P | 21 | 8/2/1978 | 5-10 | 203 | L | L | A+ | | Embry-Riddle University (Fla.) |
| | 35 | 1032 | Gregory Stokes | | 3B | 21 | 11/8/1978 | 6-1 | 183 | R | R | Rookie | | Slippery Rock University of Pennsylvania |
| | 36 | 1062 | Pedro Sanchez | | P | 18 | 6/10/1982 | 5-11 | 160 | L | L | Rookie | | Adolfina Irizarry De Puig (PR) |
| | 37 | 1092 | Chad Pylate | | P | 19 | 10/4/1980 | 6-1 | 200 | R | R | A | | Vancleave High School (Vancleave,MS) |
| | 38 | 1122 | John Lynch | | P | 19 | 5/23/1981 | 6-1 | 190 | L | L | Rookie | | Elk River High School (Rogers,MN) |
| | 39 | 1152 | Marco Gonzales | | C | | | | 0 | | | College | | Eastlake High School (Chula Vista,CA) |
| | 40 | 1182 | Scott Suraci | | LF-RF | 22 | 8/15/1977 | 6-4 | 215 | L | R | Rookie | | Hawaii Pacific University |
| | 41 | 1211 | Terry Corn | | P | 21 | 3/30/1979 | 6-2 | 215 | R | R | - | | Florida Southern College |
| | 42 | 1240** | Steve Garabrants | | 2B | 18 | 11/18/1981 | 5-10 | 175 | R | R | College | | Moon Valley High School (Phoenix,AZ) |
| | 43 | 1269** | Jeff Marquez | | P | 18 | 11/5/1981 | 6-0 | 200 | L | R | A+ | | |
| | 44 | 1297 | Brian Poetschlag | | P | | | | 0 | | | - | | Magnolia High School (Anaheim,CA) |
| | 45 | 1323 | Austin Polk | | P | | | | 0 | | | - | | Coppell High School (Coppell,TX) |
| | 46 | 1348 | Brian Baron | | OF | 21 | 9/12/1978 | 5-11 | 200 | L | R | AA | | UCLA |
| | 47 | 1372** | Peter Eberhardt | | P | 18 | 10/30/1981 | 6-3 | 215 | R | R | A- | | Whittier Christian High School (La Habra,CA) |
| | 48 | 1393 | Tanner Munsey | | C | 18 | 12/29/1981 | 6-2 | 200 | R | R | Rookie | | Oyster River High School (Durham,NH) |
| | 49 | 1413 | Ben Riley | | | | | | | | | College | | Iowa Western Community College |
| | 50 | 1433 | John Garrard | | SS | | | | 0 | | | - | | Brownsburg High School (Brownsburg,IN) |
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