| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 17 | June-Reg | David Murphy | $$ | OF | 21 | 10/18/1981 | 6-3 | 195 | L | L | MLB | 2006-2008 | Baylor University |
| 1 | 32 | June-Reg | Matt Murton | $$ | OF | 21 | 10/3/1981 | 6-1 | 226 | R | R | MLB | 2005-2008 | Georgia Tech |
| 2 | 49 | June-Reg | Abe Alvarez | $$ | P | 20 | 10/17/1982 | 6-3 | 185 | L | L | MLB | 2004-2006 | Long Beach State University |
| 2 | 54 | June-Reg | Mickey Hall | $$ | OF | 18 | 5/20/1985 | 6-0 | 180 | L | L | AA | | Walton High School (Marietta,GA) |
| 3 | 84 | June-Reg | Beau Vaughan | $$ | P | 22 | 6/4/1981 | 6-4 | 230 | B | R | AA | | Arizona State University |
| 4 | 114 | June-Reg | Jonathan Papelbon | | P | 22 | 11/23/1980 | 6-4 | 220 | R | R | MLB | 2005-2008 | Mississippi State University |
| 5 | 144 | June-Reg | Brian Marshall | | P | 20 | 8/30/1982 | 6-5 | 185 | L | L | AA | | Virginia Commonwealth University |
| 6 | 174 | June-Reg | Jessie Corn | | P | 20 | 7/16/1982 | 6-1 | 190 | R | R | A- | | Jacksonville State University |
| 7 | 204 | June-Reg | Jeremy West | | C | 21 | 11/8/1981 | 6-0 | 200 | R | R | AA | | Arizona State University |
| 8 | 234 | June-Reg | Lee Curtis | | 2B | 21 | 7/21/1981 | 5-11 | 185 | R | R | A+ | | College of Charleston |
| 9 | 264 | June-Reg | Jon Wilson | | P | 20 | 11/24/1982 | 6-0 | 210 | R | R | A | | Northeastern (Colo.) Junior College |
| 10 | 294 | June-Reg | Chris Durbin | | OF | 21 | 9/8/1981 | 6-0 | 180 | R | R | AA | | Baylor University |
| 11 | 324 | June-Reg | Barry Hertzler | | P | 22 | 2/15/1981 | 6-2 | 205 | R | R | AAA | | Central Connecticut State University |
| 12 | 354 | June-Reg | Justin Sturge | | P | 22 | 5/4/1981 | 6-4 | 190 | R | L | AA | | Coastal Carolina University |
| 13 | 384 | June-Reg | Zach Basch | | P | 22 | 6/22/1981 | 6-3 | 185 | R | R | A- | | University of Nevada |
| 14 | 414 | June-Reg | Zach Borowiak | | SS | 22 | 5/18/1981 | 6-1 | 185 | R | R | AAA | | Southeast Missouri State University |
| 15 | 444 | June-Reg | Chris Turner | | OF | 19 | 12/2/1983 | 6-0 | 190 | R | R | AA | | Texarkana College |
| 16 | 474 | June-Reg | Kevin Ool | | P | 22 | 1/4/1981 | 5-10 | 180 | L | L | AA | | Marist College |
| 17 | 504 | June-Reg | William Newton | | P | 18 | 9/3/1984 | 6-2 | 170 | L | L | Rookie | | Mountain View High School (Orem,UT) |
| 18 | 534 | June-Reg | Robert Cochran | | P | 20 | 10/16/1982 | 6-2 | 195 | L | L | A+ | | Middle Georgia College |
| 19 | 564 | June-Reg | Jarrett Gardner | | P | 22 | 3/26/1981 | 6-1 | 180 | R | R | AA | | University of Arkansas |
| 20 | 594** | June-Reg | Josh Morris | | OF | 18 | 5/11/1985 | 6-5 | 230 | R | R | A | | Cartersville High School (Cartersville,GA) |
| 21 | 624 | June-Reg | Michael Dennison | | P | 22 | 1/9/1981 | 6-0 | 200 | R | R | A+ | | Wichita State University |
| 22 | 654 | June-Reg | Kala Kaaihue | | C | 18 | 3/29/1985 | 6-1 | 225 | R | R | AA | | Iolani High School (Honolulu,HI) |
| 23 | 684 | June-Reg | David Coffey | | OF | 22 | 4/15/1981 | 5-10 | 175 | L | R | A | | University of Georgia |
| 24 | 714 | June-Reg | Ignacio Suarez | | SS | 22 | 5/3/1981 | 5-11 | 165 | R | R | AA | | Southwest Texas State University |
| 25 | 744** | June-Reg | Drew Moffitt | | OF | 21 | 8/19/1981 | 6-2 | 210 | R | R | A | | Wichita State University |
| 26 | 774 | June-Reg | Jason Ramos | | SS | 20 | 8/9/1982 | 6-0 | 185 | B | R | AA | | St. Petersburg College |
| 27 | 804 | June-Reg | Andrew Sharpe | | SS | 19 | 9/10/1983 | 6-2 | 185 | R | R | - | | Los Angeles Pierce College |
| 28 | 834 | June-Reg | Davey Penny | | P | 21 | 9/9/1981 | 6-3 | 210 | R | R | A | | East Carolina University |
| 29 | 864 | June-Reg | Douglas Fink | | P | 20 | 12/14/1982 | 6-2 | 220 | R | R | Rookie | | Manatee Community College |
| 30 | 894 | June-Reg | David Sanders | | P | 21 | 1/5/1982 | 6-4 | 195 | L | L | AAA | 2005-2005 | Wichita State University |
| 31 | 924** | June-Reg | Greg Schilling | | P | 18 | 12/21/1984 | 6-2 | 170 | L | L | - | | Taravella High School (Coral Springs,FL) |
| 32 | 954 | June-Reg | Matt Pike | | P | 18 | 10/29/1984 | 6-6 | 203 | R | R | - | | Centennial High School (Pueblo,CO) |
| 33 | 984 | June-Reg | Scooter Jordan | | OF | 22 | 12/15/1980 | 5-8 | 160 | L | R | A | | Texas Tech University |
| 34 | 1014 | June-Reg | Arthur Santos | | P | 21 | 2/20/1982 | 6-0 | 175 | R | R | AA | | Florida International University |
| 35 | 1044 | June-Reg | Erich Cloninger | | C | 22 | 11/6/1980 | 5-11 | 190 | R | R | A | | Liberty University |
| 36 | 1074 | June-Reg | Ben Sosebee | | P | 19 | 6/30/1984 | 6-4 | 180 | R | R | College | | Truett-McConnell College |
| 37 | 1104 | June-Reg | Chris Johnson | | SS | 18 | 10/1/1984 | 6-2 | 180 | R | R | - | | Bishop Verot High School (Fort Myers,FL) |
| 38 | 1134 | June-Reg | Michael McBryde | | OF | 18 | 3/22/1985 | 6-1 | 170 | R | R | A+ | | Palm Beach Gardens High School (Palm Beach Gardens,FL) |
| 39 | 1164** | June-Reg | Jeff Culpepper | | OF | 21 | 12/30/1981 | 6-1 | 180 | L | R | A+ | | Gonzaga University |
| 40 | 1194 | June-Reg | Michael Rutledge | | SS | 18 | 3/29/1985 | 6-2 | 195 | R | R | - | | Cullman High School (Cullman,AL) |
| 41 | 1224 | June-Reg | Lance Shartz | | C | 20 | 1/26/1983 | 6-1 | 205 | R | R | - | | Garden City Community College |
| 42 | 1253 | June-Reg | Dallas Williams | | OF | 18 | 11/13/1984 | 6-1 | 160 | R | R | - | | Pike High School (Indianapolis,IN) |
| 43 | 1282** | June-Reg | Scott Thomas | | C | 18 | 3/21/1985 | 5-11 | 202 | L | R | A- | | chaminade College Prep School High School (St. Louis,MO) |
| 44 | 1310** | June-Reg | Tom Caple | | OF | 22 | 8/20/1980 | 6-0 | 185 | R | R | Rookie | | University of San Diego |
| 45 | 1337 | June-Reg | Terrence Cramer | | P | 20 | 6/8/1983 | 6-3 | 235 | R | R | Rookie | | Palm Beach Community College |
| 46 | 1364 | June-Reg | Victor Rodriguez | | C | 17 | 12/4/1985 | 5-7 | 175 | R | R | - | | Cape Coral High School (Cape Coral,FL) |
| 47 | 1391 | June-Reg | A.J. Loyd | | OF | 19 | 4/6/1984 | 6-1 | 190 | R | R | - | | Bishop Carroll High School (Wichita,KS) |
| 48 | 1418 | June-Reg | Adam Davis | | P | 19 | 9/18/1983 | 6-3 | 200 | R | R | - | | Middle Georgia College |
| 49 | 1444 | June-Reg | Jason Smith | | P | 18 | 7/12/1984 | 6-3 | 196 | R | R | Rookie | | Bourne High School (Bourne,MA) |
| 50 | 1470 | June-Reg | Mitch Stachowsky | | C | 18 | 10/2/1984 | 6-3 | 220 | R | R | AAA | | College of Southern Idaho |
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