| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 13 | June-Reg | Bill Bray | $$ | P | 21 | 6/5/1983 | 6-3 | 215 | L | L | MLB | 2006-2008 | College of William and Mary |
| 2 | 54 | June-Reg | Erick San Pedro | $$ | C | 20 | 10/5/1983 | 6-0 | 205 | R | R | AAA | | University of Miami (Florida) |
| 3 | 84 | June-Reg | Ian Desmond | $$ | SS | 18 | 9/20/1985 | 6-2 | 185 | R | R | AA | | Sarasota High School (Sarasota,FL) |
| 4 | 114 | June-Reg | Collin Balester | | P | 18 | 6/6/1986 | 6-5 | 190 | R | R | AAA | | Huntington Beach High School (Huntington Beach,CA) |
| 5 | 144 | June-Reg | Greg Bunn | | P | 21 | 2/3/1983 | 6-1 | 210 | R | R | A+ | | East Carolina University |
| 6 | 174 | June-Reg | Devin Ivany | | C | 21 | 7/27/1982 | 6-1 | 178 | R | R | AA | | University of South Florida |
| 7 | 204 | June-Reg | Marvin Lowrance | | OF | 19 | 7/16/1984 | 6-0 | 215 | L | L | A+ | | Golden West College |
| 8 | 234 | June-Reg | Leonard Davis | | 3B | 20 | 12/24/1983 | 5-10 | 195 | L | R | A+ | | Fresno City College |
| 9 | 264 | June-Reg | Brandon Conway | | SS | 20 | 11/9/1983 | 6-3 | 190 | L | R | A- | | Frederick Community College |
| 10 | 294 | June-Reg | Duron Legrande | | OF | 23 | 6/6/1981 | 6-2 | 185 | L | L | A- | | North Carolina A&T State University |
| 11 | 324 | June-Reg | David Trahan | | P | 23 | 2/27/1981 | 6-3 | 185 | R | R | AA | | Alvin Community College |
| 12 | 354** | June-Reg | Robert Mosebach | | OF | 19 | 9/14/1984 | 6-4 | 195 | R | R | AA | | Hillsborough Community College |
| 13 | 384 | June-Reg | David Travis | | 2B | 23 | 12/15/1980 | 6-4 | 210 | L | R | A- | | Southern Wesleyan University (S.C.) |
| 14 | 414 | June-Reg | Lyndsey Simmons | | C | 22 | 10/15/1981 | 6-0 | 200 | L | R | Ind | | New York Tech |
| 15 | 444** | June-Reg | Mike Wlodarczyk | | P | 21 | 12/2/1982 | 6-5 | 230 | L | L | AA | | Boston College |
| 16 | 474 | June-Reg | Thomas Wilson | | P | 22 | 5/21/1982 | 6-2 | 185 | R | L | A+ | | Catawba College. |
| 17 | 504 | June-Reg | John Poppert | | C | 22 | 4/14/1982 | 6-1 | 210 | R | R | A+ | | East Carolina University |
| 18 | 534 | June-Reg | Matt Perks | | P | 18 | 8/20/1985 | 6-7 | 200 | R | R | A | | Mercer County Community College |
| 19 | 564 | June-Reg | Ben Cox | | P | 22 | 9/20/1981 | 6-2 | 210 | L | R | AA | | Lamar University |
| 20 | 594 | June-Reg | Wendell Yost | | P | 23 | 6/23/1981 | 6-3 | 185 | R | L | A+ | | Averett University |
| 21 | 624** | June-Reg | Ibrahim Lopez | | OF | | | | | | | - | | Puerto Rico Baseball Academy High School (Gurabo,PR) |
| 22 | 654 | June-Reg | Aaron Jackson | | P | 18 | 3/28/1986 | 6-0 | 175 | B | R | A | | St. Augustine High School (St. Augustine,FL) |
| 23 | 684 | June-Reg | Ryan Harrison | | P | 17 | 7/12/1986 | 6-2 | 190 | R | R | A | | South Carroll High School (Sykesville,MD) |
| 24 | 714 | June-Reg | Steven Hornostaj | | SS | | | | | | | - | | St. David Catholic High School (Waterloo,ON) |
| 25 | 744 | June-Reg | Steven Cook | | P | 22 | 11/26/1981 | 6-4 | 205 | R | R | A | | University of North Carolina-Asheville |
| 26 | 774 | June-Reg | Gabe Suarez | | SS | 19 | 12/14/1984 | 6-0 | 185 | R | R | A+ | | South Mountain Community College |
| 27 | 804 | June-Reg | Ladd Hall | | P | | | | 0 | | | - | | Arizona State University |
| 28 | 834 | June-Reg | Chris Lugo | | P | 17 | 11/10/1986 | 6-1 | 185 | R | R | A+ | | Hudson Catholic High School (Jersey City,NJ) |
| 29 | 864** | June-Reg | Steven Hirschfeld | | P | 18 | 9/8/1985 | 6-5 | 220 | R | R | A | | Grand County High School (Moab,UT) |
| 30 | 894 | June-Reg | Brendan Murphy | | 1B | 19 | 10/7/1984 | 6-3 | 210 | R | R | College | | Garden City Community College |
| 31 | 924** | June-Reg | P.J. Treadaway | | P | | | | | | | College | | Archbishop Hannan High School (Meraux,LA) |
| 32 | 954** | June-Reg | Matt Averitt | | P | | | | | | | - | | New Mexico Junior College |
| 33 | 984 | June-Reg | Chris Whisenhunt | | P | | | | | | | - | | Fort Worth Christian High School (North Richland Hills,TX) |
| 34 | 1014 | June-Reg | Richard Campbell | | P | 22 | 10/17/1981 | 6-0 | 175 | R | R | MLB | 2006-2006 | Kennesaw State University |
| 35 | 1044 | June-Reg | Rudy Garza | | P | 20 | 4/10/1984 | 6-2 | 190 | R | R | A | | Hill College |
| 36 | 1074 | June-Reg | Todd Nicholas | | P | 21 | 7/30/1982 | 6-2 | 208 | R | L | College | | Troy State University |
| 37 | 1104** | June-Reg | Jamie Gant | | P | 21 | 9/14/1982 | 6-2 | 190 | R | R | A | | Mississippi State University |
| 38 | 1134 | June-Reg | Daniel Cooper | | P | 17 | 11/6/1986 | 6-3 | 203 | R | R | College | | Costa Mesa High School (Costa Mesa,CA) |
| 39 | 1164 | June-Reg | Brian Peacock | | C | 19 | 8/26/1984 | 5-11 | 181 | R | R | A+ | | Manatee Community College |
| 40 | 1194 | June-Reg | Melvin Perez | | 3B | | | | | | | Rookie | | |
| 41 | 1224 | June-Reg | Joseph Dunigan | | OF | | | | | | | - | | St. Ignatius College Prep High School (Chicago,IL) |
| 42 | 1253 | June-Reg | Brent Gaphardt | | P | | | | | | | College | | Dundalk Community College |
| 43 | 1282 | June-Reg | Andy Gale | | P | | | | | | | College | | Phillips Exeter Academy High School (Exeter,NH) |
| 44 | 1311 | June-Reg | Phillip Valle | | SS | | | | | | | - | | Bellevue Christian High School (Clyde Hill,WA) |
| 45 | 1340 | June-Reg | Austin Reilly | | SS | | | | | | | College | | Fort Worth Country Day High School (Fort Worth,TX) |
| 46 | 1369 | June-Reg | Robert Molinaro | | SS | | | | | | | - | | American Heritage High School (Delray Beach,FL) |
| 47 | 1398 | June-Reg | Jonathan Del Franco | | P | | | | | | | - | | Bridgewater Raritan High School (Bridgewater,NJ) |
| 48 | 1427 | June-Reg | Carlos Ceron | | P | | | | | | | - | | Miami-Dade College |
| 49 | 1455 | June-Reg | Patrick Kanakevich | | P | | | | | | | - | | Georgetown Prep High School (North Bethesda,MD) |
| 50 | 1483 | June-Reg | Joel Collins | | C | | | | | | | - | | Cardinal Carter High School (Richmond Hill,ON) |
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