| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 4 | June-Reg | Gavin Floyd | $$ | P | 18 | 1/27/1983 | 6-5 | 210 | R | R | MLB | 2004-2008 | Mount St. Joseph High School (Severna Park,MD) |
| 4 | 110 | June-Reg | Terry Jones | | IF | 18 | 3/20/1983 | 6-2 | 190 | R | R | A+ | | Upland High School (Upland,CA) |
| 5 | 140 | June-Reg | Ryan Howard | | 1B | 21 | 11/19/1979 | 6-4 | 230 | L | L | MLB | 2004-2008 | Southwest Missouri State University |
| 6 | 170 | June-Reg | Bryan Hansen | | 1B | 18 | 5/8/1983 | 6-2 | 205 | L | L | AA | | Longwood High School (Middle Island,NY) |
| 7 | 200 | June-Reg | Vinnie DeChristofaro | | P | 19 | 4/2/1982 | 6-1 | 170 | L | L | A | | Richmond Hill High School (Richmond Hill,GA) |
| 8 | 230 | June-Reg | Taft Cable | | P | 20 | 7/25/1980 | 6-2 | 210 | R | R | AA | | University of North Carolina-Greensboro |
| 9 | 260 | June-Reg | Chris Roberson | | OF | 21 | 8/23/1979 | 6-2 | 175 | R | R | MLB | 2006-2007 | Feater River College |
| 10 | 290** | June-Reg | Rocky Cherry | | P | 21 | 8/19/1979 | 6-5 | 210 | R | R | MLB | 2007-2007 | University of Oklahoma |
| 11 | 320 | June-Reg | Matt Sweeney | | P | 18 | 2/25/1983 | 6-2 | 180 | R | R | AA | | Steinert High School (Trenton,NJ) |
| 12 | 350 | June-Reg | Rod Perry | | OF | 22 | 2/1/1979 | 5-10 | 195 | R | R | A+ | | Penn State University |
| 13 | 380 | June-Reg | Andre Marshall | | OF | 20 | 12/2/1980 | 6-5 | 205 | B | R | A | | University of Washington |
| 14 | 410 | June-Reg | Mario Delgado | | IF | 21 | 8/5/1979 | 6-0 | 220 | L | L | AA | | Oklahoma City University |
| 15 | 440 | June-Reg | Tim Davis | | P | 22 | 4/8/1979 | 6-4 | 230 | L | L | A | | University of South Alabama |
| 16 | 470 | June-Reg | Ben Margalski | | C | 21 | 9/2/1979 | 6-2 | 210 | L | R | A+ | | Southwest Missouri State University |
| 17 | 500 | June-Reg | Ryan Hutchison | | P | 22 | 8/9/1978 | 6-0 | 205 | R | R | AAA | | Western Kentucky University |
| 18 | 530 | June-Reg | Ben Ally | | P | 22 | 2/9/1979 | 6-2 | 205 | R | R | A- | | Warner Southern College (Fla.) |
| 19 | 560 | June-Reg | Matt Squires | | P | 22 | 1/24/1979 | 5-10 | 200 | L | L | AA | | Whitworth College |
| 20 | 590 | June-Reg | Vince Vukovich | | OF | 21 | 5/6/1980 | 6-0 | 175 | L | R | A+ | | University of Delaware |
| 21 | 620** | June-Reg | Julian Williams | | CF | 17 | 7/27/1983 | 5-11 | 175 | R | R | A | | Upland High School (Upland,CA) |
| 22 | 650 | June-Reg | Michael Floyd | | | 21 | 1/15/1980 | 6-3 | 185 | R | R | A+ | | University of South Carolina |
| 23 | 680 | June-Reg | Joshua Cisneros | | C | 21 | 11/9/1979 | 5-10 | 190 | R | R | Ind | | West Virginia University |
| 24 | 710 | June-Reg | Kris Lammers | | | 22 | 12/7/1978 | 6-2 | 195 | L | L | Rookie | | Middle Tennessee State University |
| 25 | 740 | June-Reg | Josh Scott | | P | 21 | 10/24/1979 | 6-3 | 190 | L | L | A | | Baylor University |
| 26 | 770 | June-Reg | Layne Dawson | | P | 21 | 9/13/1979 | 6-2 | 180 | R | R | AA | | University of Memphis |
| 27 | 800 | June-Reg | Jay Bernard | | P | 22 | 8/14/1978 | 6-5 | 220 | R | R | A | | Troy State University |
| 28 | 830 | June-Reg | Michael Nall | | | 22 | 5/1/1979 | 6-1 | 190 | R | R | A- | | Northwestern University |
| 29 | 860 | June-Reg | Jeremy Kurella | | | 22 | 1/18/1979 | 6-1 | 190 | B | R | College | | University of Central Florida |
| 30 | 890 | June-Reg | Kris Bennett | | 3B | 21 | 10/3/1979 | 5-10 | 170 | R | R | A+ | | University of Tennessee |
| 31 | 920 | June-Reg | Gabrial Johnston | | C | | | | 0 | | | - | | Sonoma State University |
| 32 | 950 | June-Reg | Josh Miller | | P | 22 | 2/7/1979 | 6-1 | 200 | R | R | AAA | | North Carolina State University |
| 33 | 980 | June-Reg | Daniel McCall | | P | 22 | 6/5/1979 | 6-0 | 175 | L | L | Rookie | | Penn State University |
| 34 | 1010 | June-Reg | Brian Schriner | | | 22 | 9/4/1978 | 6-3 | 215 | R | R | Rookie | | University of Louisiana-Monroe |
| 35 | 1040 | June-Reg | Nick Glaser | | P | 22 | 7/12/1978 | 6-2 | 190 | R | R | A- | | Clemson University |
| 36 | 1070 | June-Reg | Jeff Phelps | | IF | 22 | 11/20/1978 | 6-0 | 195 | R | R | AA | | Arizona State University |
| 37 | 1100 | June-Reg | Wes Carroll | | 2B | 22 | 1/25/1979 | 5-11 | 185 | R | R | AAA | - | University of Evansville |
| 38 | 1130 | June-Reg | Jaime Martinez | | | | | | | | | Ind | | Hueneme High School (Oxnard,CA) |
| 39 | 1160** | June-Reg | Jason Jaramillo | | | 18 | 10/9/1982 | 6-0 | 200 | B | R | AAA | | Case High School (Racine,WI) |
| 40 | 1190** | June-Reg | Arnold Hughey | | | 18 | 11/19/1982 | 6-2 | 215 | L | L | A- | | Venice High School (Venice,FL) |
| 41 | 1219 | June-Reg | Dustin Miller | | P | | | | | | | Rookie | | Diamond Bar High School (Diamond Bar,CA) |
| 42 | 1248** | June-Reg | Will Thompson | | | 18 | 11/20/1982 | 6-1 | 180 | L | L | AAA | | Loyola-Sacred Heart High School (Missoula,MT) |
| 43 | 1276** | June-Reg | Andy Lytle | | | 18 | 9/15/1982 | 6-1 | 165 | R | R | A | | Highlands Ranch High School (Highlands Ranch,CO) |
| 44 | 1304 | June-Reg | Humberto Gonzales | | SS-2B | 20 | 3/6/1981 | 5-10 | 155 | R | R | - | | Rainier Beach High School (Seattle,WA) |
| 45 | 1332 | June-Reg | Jared Birrenkott | | C | 18 | 11/25/1982 | 6-3 | 205 | L | R | College | | Granite Hills High School (El Cajon,CA) |
| 46 | 1360 | June-Reg | Allen Hicks | | OF | | | | 0 | | | - | | King High School (Tampa,FL) |
| 47 | 1388 | June-Reg | Sean Walsh | | 3B | 21 | 11/15/1979 | 6-4 | 220 | R | R | AA | - | North Carolina State University |
| 48 | 1415 | June-Reg | Maximo Reyes | | P | 19 | 9/24/1981 | 5-9 | 170 | R | R | A+ | | St. Petersburg College |
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