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| | 1 | 9 | Mike Pelfrey | | rhp | 21 | 1/14/1984 | 6-7 | 190 | R | R | MLB | 2006-2007 | Wichita State University |
| | 4 | 119 | Hector Pellot | | 2b | 18 | 2/8/1987 | 5-11 | 184 | R | R | A+ | | Puerto Rico Baseball Academy High School (Gurabo,PR) |
| | 5 | 149 | Drew Butera | | c | 21 | 8/9/1983 | 6-1 | 190 | R | R | AA | | University of Central Florida |
| | 6 | 179 | Greg Cain | | of | 18 | 5/1/1987 | 6-1 | 205 | R | R | Rookie | | Gahr High School (Cerritos,CA) |
| | 7 | 209 | Jon Niese | | LHP | 18 | 10/27/1986 | 6-3 | 190 | L | L | A+ | | Defiance High School (Defiance,OH) |
| | 8 | 239 | Sean McCraw | | C | 19 | 3/11/1986 | 6-0 | 185 | L | R | A+ | | San Jacinto College-North |
| | 9 | 269 | Robert Parnell | | rhp | 20 | 9/8/1984 | 6-3 | 180 | R | R | AA | | Charleston Southern University |
| | 10 | 299 | Courtney Billingslea | | OF | 19 | 2/16/1986 | 6-6 | 205 | R | R | Rookie | | Sinclair Community College |
| | 11 | 329 | Luis Martinez | | c | 20 | 4/3/1985 | 6-0 | 210 | R | R | A | | Jackson State Community College |
| | 12 | 359 | Matthew Spath | | of | 18 | 10/21/1986 | 6-1 | 185 | R | R | Rookie | | Flagler Palm Coast High School (Bunnell,FL) |
| | 13 | 389 | Joshua Thole | | c | 18 | 10/28/1986 | 6-1 | 190 | L | R | A | | Mater Dei High School (Breese,IL) |
| | 14 | 419 | Ian Marshall | | RHP | 18 | 3/3/1987 | 6-3 | 172 | R | R | College | | Gaithersburg High School (Gaithersburg,MD) |
| | 15 | 449 | Daniel Martin | | RHP | 18 | 6/21/1987 | 6-8 | 230 | R | R | - | | Harleton High School (Marshall,TX) |
| | 16 | 479 | Eric Domangue | | lhp | 20 | 8/16/1984 | 6-5 | 200 | L | L | A | | Alvin Community College |
| | 17 | 509** | Pedro Beato | | RHP | 18 | 10/27/1986 | 6-5 | 210 | R | R | A | | Xavieran High School (Brooklyn,NY) |
| | 18 | 539 | Jeff Brown | | rhp | | | | | | | College | | Wingate University |
| | 19 | 569 | Tim Grogan | | 3b | 21 | 3/30/1984 | 6-0 | 195 | L | R | A- | | Western Kentucky University |
| | 20 | 599 | Cody Railsback | | rhp | 18 | 6/3/1987 | 6-3 | 160 | R | R | A | | Ryan High School (Denton,TX) |
| | 21 | 629 | Joe Holden | | OF | 21 | 4/10/1984 | 5-11 | 175 | L | R | A | | Molloy College |
| | 22 | 659 | Preston Paramore | | c | 18 | 10/30/1986 | 6-3 | 205 | B | R | College | | Allen High School (Allen,TX) |
| | 23 | 689 | Joe D'Alessandro | | rhp | 21 | 2/20/1984 | 5-11 | 195 | R | R | A | | The College of New Jersey |
| | 24 | 719 | Kyle Risinger | | RHP | 20 | 8/15/1984 | 6-4 | 200 | R | R | A- | | Galveston College |
| | 25 | 749 | D.J. Wabick | | 1b | 21 | 5/30/1984 | 6-2 | 185 | L | R | A | | College of Charleston |
| | 26 | 779 | Kevin Tomasiewicz | | LHP | 21 | 9/17/1983 | 6-2 | 225 | L | L | AA | | University of Wisconsin, Whitewater |
| | 27 | 809 | David Koons | | rhp | 21 | 3/13/1984 | 6-1 | 180 | R | R | A | | Saint Leo University |
| | 28 | 839 | Greg Gonzalez | | of | 22 | 10/1/1982 | 5-11 | 165 | L | L | A- | | California State University, Chico |
| | 29 | 869 | Sal Aguilar | | RHP | 23 | 1/9/1982 | 6-0 | 190 | R | R | AA | | Lewis-Clark State College (Idaho) |
| | 30 | 899 | Steve Holquin | | rhp | 20 | 6/30/1985 | 6-3 | 215 | R | R | Rookie | | Porterville (Calif.) Junior College |
| | 31 | 929 | Matt Anderson | | 3b | 22 | 12/9/1982 | 6-2 | 205 | L | R | A | | University of California-Irvine |
| | 32 | 959 | Jose Castro | | SS | 18 | 11/5/1986 | 5-8 | 160 | B | R | AA | | Miami-Dade College |
| | 33 | 989 | Daniel Arizmendi | | lhp | 21 | 6/13/1984 | 5-11 | 200 | L | L | Rookie | | Santa Ana College |
| | 34 | 1019 | Joe Mihalics | | 2B | 22 | 4/7/1983 | 5-9 | 170 | R | R | A | | University of Buffalo |
| | 35 | 1049 | Michael Sharpe | | of | 22 | 3/10/1983 | 6-0 | 190 | L | R | A- | | St. Thomas Aquinas College |
| | 36 | 1079 | Jeramy Simmons | | rhp | 22 | 9/30/1982 | 6-0 | 200 | R | R | AA | | University of South Alabama |
| | 37 | 1109 | Alexis Beras | | RHP | 21 | 9/24/1983 | 6-5 | 215 | R | R | A+ | | University of Scranton |
| | 38 | 1139 | Pierre Miville-Deschenes | | rhp | 19 | 5/23/1986 | 6-2 | 190 | R | R | - | | Edouard Montpetit High School (Montreal,QC) |
| | 39 | 1169 | Colin Thomson | | rhp | 18 | 2/12/1987 | 6-4 | 195 | R | R | - | | Mountain View High School (Mesa,AZ) |
| | 40 | 1198** | Jacob Blackwood | | 2B | 19 | 9/14/1985 | 6-0 | 195 | R | R | A | | Maple Woods Community College |
| | 41 | 1227 | Nick Carr | | rhp | 18 | 4/19/1987 | 6-1 | 195 | R | R | A- | | Twin Falls High School (Twin Falls,ID) |
| | 42 | 1256 | Jared Barkdoll | | C | 18 | 8/19/1986 | 6-2 | 185 | R | R | - | | Greencastle-Antrim High School (Greencastle,PA) |
| | 43 | 1285 | Javier Brown | | ss | 18 | 6/24/1987 | 5-9 | 175 | R | R | - | | Valhalla High School (El Cajon,CA) |
| | 44 | 1314 | Phillip Pursino | | c | 17 | 7/8/1987 | 5-11 | 175 | R | R | College | | St. Dominic's High School (Oyster Bay,NY) |
| | 45 | 1343 | Anthony Manuel | | 2B | | | | 0 | | | A | - | Biola University (Calif.) |
| | 46 | 1372** | Peter Tountas | | SS | 17 | 7/1/1987 | 6-2 | 175 | R | R | - | | Maine South High School (Park Ridge,IL) |
| | 47 | 1401 | Samuel Lane | | rhp | 18 | 12/16/1986 | 6-2 | 175 | R | R | - | | Pedro Menendez High School (Elkton,FL) |
| | 48 | 1429 | Jeremy Hefner | | rhp | 19 | 3/11/1986 | 6-4 | | R | R | A- | | Seminole State College |
| | 49 | 1456 | Will Jostock | | rhp | 18 | 9/10/1986 | 6-6 | 190 | R | R | Rookie | | Pensacola Junior College |
| | 50 | 1483 | Julio Rodriguez | | OF | 18 | 1/14/1987 | 6-3 | 185 | R | R | - | | Wabash Valley College |
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