| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 9 | June-Reg | Mike Pelfrey | | rhp | 21 | 1/14/1984 | 6-7 | 190 | R | R | MLB | 2006-2008 | Wichita State University |
| 4 | 119 | June-Reg | Hector Pellot | | 2b | 18 | 2/8/1987 | 5-11 | 184 | R | R | A+ | | Puerto Rico Baseball Academy High School (Gurabo,PR) |
| 5 | 149 | June-Reg | Drew Butera | | c | 21 | 8/9/1983 | 6-1 | 190 | R | R | AA | | University of Central Florida |
| 6 | 179 | June-Reg | Greg Cain | | of | 18 | 5/1/1987 | 6-1 | 205 | R | R | Rookie | | Richard Gahr High School (Cerritos,CA) |
| 7 | 209 | June-Reg | Jon Niese | | LHP | 18 | 10/27/1986 | 6-3 | 190 | L | L | AA | | Defiance High School (Defiance,OH) |
| 8 | 239 | June-Reg | Sean McCraw | | C | 19 | 3/11/1986 | 6-0 | 185 | L | R | A+ | | San Jacinto College-North |
| 9 | 269 | June-Reg | Robert Parnell | | rhp | 20 | 9/8/1984 | 6-3 | 180 | R | R | AA | | Charleston Southern University |
| 10 | 299 | June-Reg | Courtney Billingslea | | OF | 19 | 2/16/1986 | 6-6 | 205 | R | R | Rookie | | Sinclair Community College |
| 11 | 329 | June-Reg | Luis Martinez | | c | 20 | 4/3/1985 | 6-0 | 210 | R | R | A | | Jackson State Community College |
| 12 | 359 | June-Reg | Matthew Spath | | of | 18 | 10/21/1986 | 6-1 | 185 | R | R | Rookie | | Flagler Palm Coast High School (Bunnell,FL) |
| 13 | 389 | June-Reg | Joshua Thole | | c | 18 | 10/28/1986 | 6-1 | 190 | L | R | A+ | | Mater Dei High School (Breese,IL) |
| 14 | 419 | June-Reg | Ian Marshall | | RHP | 18 | 3/3/1987 | 6-3 | 172 | R | R | College | | Gaithersburg High School (Gaithersburg,MD) |
| 15 | 449 | June-Reg | Daniel Martin | | RHP | 18 | 6/21/1987 | 6-9 | 265 | R | R | - | | Harleton High School (Marshall,TX) |
| 16 | 479 | June-Reg | Eric Domangue | | lhp | 20 | 8/16/1984 | 6-5 | 200 | L | L | A | | Alvin Community College |
| 17 | 509** | June-Reg | Pedro Beato | | RHP | 18 | 10/27/1986 | 6-5 | 210 | R | R | A+ | | Xavieran High School (Brooklyn,NY) |
| 18 | 539 | June-Reg | Jeff Brown | | rhp | | | | | | | College | | Wingate University |
| 19 | 569 | June-Reg | Tim Grogan | | 3b | 21 | 3/30/1984 | 6-0 | 195 | L | R | A- | | Western Kentucky University |
| 20 | 599 | June-Reg | Cody Railsback | | rhp | 18 | 6/3/1987 | 6-3 | 160 | R | R | A | | Ryan High School (Denton,TX) |
| 21 | 629 | June-Reg | Joe Holden | | OF | 21 | 4/10/1984 | 5-11 | 175 | L | R | A+ | | Molloy College |
| 22 | 659 | June-Reg | Preston Paramore | | c | 18 | 10/30/1986 | 6-3 | 205 | B | R | College | | Allen High School (Allen,TX) |
| 23 | 689 | June-Reg | Joe D'Alessandro | | rhp | 21 | 2/20/1984 | 5-11 | 195 | R | R | A | | The College of New Jersey |
| 24 | 719 | June-Reg | Kyle Risinger | | RHP | 20 | 8/15/1984 | 6-4 | 200 | R | R | A- | | Galveston College |
| 25 | 749 | June-Reg | D.J. Wabick | | 1b | 21 | 5/30/1984 | 6-2 | 185 | L | R | A+ | | College of Charleston |
| 26 | 779 | June-Reg | Kevin Tomasiewicz | | LHP | 21 | 9/17/1983 | 6-2 | 225 | L | L | AA | | University of Wisconsin, Whitewater |
| 27 | 809 | June-Reg | David Koons | | rhp | 21 | 3/13/1984 | 6-1 | 180 | R | R | A | | Saint Leo University |
| 28 | 839 | June-Reg | Greg Gonzalez | | of | 22 | 10/1/1982 | 5-11 | 165 | L | L | A- | | California State University, Chico |
| 29 | 869 | June-Reg | Sal Aguilar | | RHP | 23 | 1/9/1982 | 6-0 | 190 | R | R | AA | | Lewis-Clark State College (Idaho) |
| 30 | 899 | June-Reg | Steve Holquin | | rhp | 20 | 6/30/1985 | 6-3 | 215 | R | R | Rookie | | Porterville (Calif.) Junior College |
| 31 | 929 | June-Reg | Matt Anderson | | 3b | 22 | 12/9/1982 | 6-2 | 205 | L | R | A | | University of California-Irvine |
| 32 | 959 | June-Reg | Jose Castro | | SS | 18 | 11/5/1986 | 5-8 | 160 | B | R | AA | | Miami-Dade College |
| 33 | 989 | June-Reg | Daniel Arizmendi | | lhp | 21 | 6/13/1984 | 5-11 | 200 | L | L | Rookie | | Santa Ana College |
| 34 | 1019 | June-Reg | Joe Mihalics | | 2B | 22 | 4/7/1983 | 5-9 | 170 | R | R | A | | University of Buffalo |
| 35 | 1049 | June-Reg | Michael Sharpe | | of | 22 | 3/10/1983 | 6-0 | 190 | L | R | A- | | St. Thomas Aquinas College |
| 36 | 1079 | June-Reg | Jeramy Simmons | | rhp | 22 | 9/30/1982 | 6-0 | 200 | R | R | AA | | University of South Alabama |
| 37 | 1109 | June-Reg | Alexis Beras | | RHP | 21 | 9/24/1983 | 6-5 | 215 | R | R | A+ | | University of Scranton |
| 38 | 1139 | June-Reg | Pierre Miville-Deschenes | | rhp | 19 | 5/23/1986 | 6-2 | 190 | R | R | - | | Edouard Montpetit High School (Montreal,QC) |
| 39 | 1169 | June-Reg | Colin Thomson | | rhp | 18 | 2/12/1987 | 6-4 | 195 | R | R | - | | Mountain View High School (Mesa,AZ) |
| 40 | 1198** | June-Reg | Jacob Blackwood | | 2B | 19 | 9/14/1985 | 6-0 | 195 | R | R | A+ | | Maple Woods Community College |
| 41 | 1227 | June-Reg | Nick Carr | | rhp | 18 | 4/19/1987 | 6-1 | 195 | R | R | A+ | | Twin Falls High School (Twin Falls,ID) |
| 42 | 1256 | June-Reg | Jared Barkdoll | | C | 18 | 8/19/1986 | 6-2 | 185 | R | R | - | | Greencastle-Antrim High School (Greencastle,PA) |
| 43 | 1285 | June-Reg | Javier Brown | | ss | 18 | 6/24/1987 | 6-0 | 175 | R | R | - | | Valhalla High School (El Cajon,CA) |
| 44 | 1314 | June-Reg | Phillip Pursino | | c | 17 | 7/8/1987 | 5-11 | 175 | R | R | College | | St. Dominic's High School (Oyster Bay,NY) |
| 45 | 1343 | June-Reg | Anthony Manuel | | 2B | | | | 0 | | | A | - | Biola University (Calif.) |
| 46 | 1372** | June-Reg | Peter Tountas | | SS | 17 | 7/1/1987 | 6-2 | 175 | R | R | - | | Maine South High School (Park Ridge,IL) |
| 47 | 1401 | June-Reg | Samuel Lane | | rhp | 18 | 12/16/1986 | 6-2 | 175 | R | R | - | | Pedro Menendez High School (Elkton,FL) |
| 48 | 1429 | June-Reg | Jeremy Hefner | | rhp | 19 | 3/11/1986 | 6-4 | | R | R | A | | Seminole State College |
| 49 | 1456 | June-Reg | Will Jostock | | rhp | 18 | 9/10/1986 | 6-6 | 190 | R | R | Rookie | | Pensacola Junior College |
| 50 | 1483 | June-Reg | Julio Rodriguez | | OF | 18 | 1/14/1987 | 6-3 | 185 | R | R | - | | Wabash Valley College |
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