| 1 | 9 | June-Reg | Mike Pelfrey | P | 21 | 6-7 | 190 | R | R | MLB | 2006-2009 | Wichita State University | $3,550,000 |
| 4 | 119 | June-Reg | Hector Pellot | 2b | 18 | 5-11 | 184 | R | R | A+ | | Puerto Rico Baseball Academy (Gurabo,PR) | $350,000 |
| 5 | 149 | June-Reg | Drew Butera | c | 21 | 6-1 | 190 | R | R | AAA | | University of Central Florida | $175,000 |
| 6 | 179 | June-Reg | Greg Cain | of | 18 | 6-1 | 205 | R | R | Rookie | | Gahr (Cerritos,CA) | $152,500 |
| 7 | 209 | June-Reg | Jon Niese | P | 18 | 6-3 | 190 | L | L | MLB | 2008-2009 | Defiance (Defiance,OH) | $175,000 |
| 8 | 239 | June-Reg | Sean McCraw | C | 19 | 6-0 | 185 | L | R | A+ | | San Jacinto College | $150,000 |
| 9 | 269 | June-Reg | Robert Parnell | P | 20 | 6-3 | 180 | R | R | MLB | 2008-2009 | Charleston Southern University | $65,000 |
| 10 | 299 | June-Reg | Courtney Billingslea | OF | 19 | 6-6 | 205 | R | R | Ind | | Sinclair Community College | $60,000 |
| 11 | 329 | June-Reg | Luis Martinez | c | 20 | 6-0 | 210 | R | R | AAA | | Jackson State Community College | |
| 12 | 359 | June-Reg | Matthew Spath | of | 18 | 6-1 | 185 | R | R | Rookie | | Flagler Palm Coast (Bunnell,FL) | |
| 13 | 389 | June-Reg | Josh Thole | c | 18 | 6-1 | 190 | L | R | MLB | 2009-2009 | Mater Dei (Breese,IL) | |
| 14 | 419 | June-Reg | Ian Marshall | P | 18 | 6-3 | 172 | R | R | College | | Gaithersburg (Gaithersburg,MD) | |
| 15 | 449 | June-Reg | Daniel Martin | P | 18 | 6-9 | 265 | R | R | College | | Harleton (Marshall,TX) | |
| 16 | 479 | June-Reg | Eric Domangue | P | 20 | 6-5 | 200 | L | L | A | | Alvin Community College | |
| 17 | 509** | June-Reg | Pedro Beato | P | 18 | 6-5 | 210 | R | R | AA | | Xaverian (Brooklyn,NY) | $0 |
| 18 | 539 | June-Reg | Eric Brown | P | 21 | 6-4 | 228 | R | R | AA | | Wingate University | |
| 19 | 569 | June-Reg | Tim Grogan | 3b | 21 | 6-0 | 195 | L | R | A- | | Western Kentucky University | |
| 20 | 599 | June-Reg | Cody Railsback | P | 18 | 6-3 | 160 | R | R | A | | Ryan (Denton,TX) | |
| 21 | 629 | June-Reg | Joe Holden | OF | 21 | 5-11 | 175 | L | R | A+ | | Molloy College | |
| 22 | 659 | June-Reg | Preston Paramore | c | 18 | 6-3 | 205 | B | R | A | | Allen (Allen,TX) | |
| 23 | 689 | June-Reg | Joe D'Alessandro | P | 21 | 5-11 | 195 | R | R | A | | The College of New Jersey | |
| 24 | 719 | June-Reg | Kyle Risinger | P | 20 | 6-4 | 200 | R | R | A- | | Galveston College | |
| 25 | 749 | June-Reg | D.J. Wabick | 1b | 21 | 6-2 | 185 | L | R | AA | | College of Charleston | |
| 26 | 779 | June-Reg | Doak Tomasiewicz | P | 21 | 6-2 | 225 | L | L | AA | | University of Wisconsin-Whitewater | |
| 27 | 809 | June-Reg | David Koons | P | 21 | 6-1 | 180 | R | R | A | | Saint Leo University | |
| 28 | 839 | June-Reg | Greg Gonzalez | of | 22 | 5-11 | 165 | L | L | A- | | Chico State | |
| 29 | 869 | June-Reg | Sal Aguilar | P | 23 | 6-0 | 190 | R | R | AA | | Lewis-Clark State College | |
| 30 | 899 | June-Reg | Steve Holquin | P | 20 | 6-3 | 215 | R | R | Rookie | | Porterville College | |
| 31 | 929 | June-Reg | Matt Anderson | 3b | 22 | 6-2 | 205 | L | R | A | | University of California-Irvine | |
| 32 | 959 | June-Reg | Jose Castro | SS | 18 | 5-8 | 160 | B | R | AA | | Miami-Dade College | |
| 33 | 989 | June-Reg | Daniel Arizmendi | P | 21 | 5-11 | 200 | L | L | Ind | | Santa Ana College | |
| 34 | 1019 | June-Reg | Joe Mihalics | 2B | 22 | 5-9 | 170 | R | R | A | | University at Buffalo | |
| 35 | 1049 | June-Reg | Michael Sharpe | of | 22 | 6-0 | 190 | L | R | A- | | St. Thomas Aquinas College | |
| 36 | 1079 | June-Reg | Jeramy Simmons | P | 22 | 6-0 | 200 | R | R | AA | | University of South Alabama | |
| 37 | 1109 | June-Reg | Alexis Beras | P | 21 | 6-5 | 215 | R | R | A+ | | University of Scranton | |
| 38 | 1139 | June-Reg | Pierre Miville-Deschenes | P | 19 | 6-2 | 190 | R | R | - | | Edouard Montpetit (Montreal,QC) | |
| 39 | 1169 | June-Reg | Colin Thomson | P | 18 | 6-4 | 195 | R | R | - | | Mountain View (Mesa,AZ) | |
| 40 | 1198** | June-Reg | Jacob Blackwood | 2B | 19 | 6-0 | 195 | R | R | A+ | | Maple Woods Community College | |
| 41 | 1227 | June-Reg | Nick Carr | P | 18 | 6-1 | 195 | R | R | A+ | | Twin Falls (Twin Falls,ID) | |
| 42 | 1256 | June-Reg | Jared Barkdoll | C | 18 | 6-2 | 185 | R | R | - | | Greencastle-Antrim (Greencastle,PA) | |
| 43 | 1285 | June-Reg | Javier Brown | ss | 18 | 6-0 | 175 | R | R | Rookie | | Valhalla (El Cajon,CA) | |
| 44 | 1314 | June-Reg | Phillip Pursino | c | 17 | 5-11 | 175 | R | R | College | | St. Dominic's (Oyster Bay,NY) | |
| 45 | 1343 | June-Reg | Anthony Manuel | 2B | | | 0 | | | A | - | Biola University | |
| 46 | 1372** | June-Reg | Peter Tountas | SS | 17 | 6-2 | 175 | R | R | College | | Maine South (Park Ridge,IL) | |
| 47 | 1401 | June-Reg | Samuel Lane | P | 18 | 6-2 | 175 | R | R | - | | Pedro Menendez (Elkton,FL) | |
| 48 | 1429 | June-Reg | Jeremy Hefner | P | 19 | 6-4 | | R | R | AAA | | Seminole State College | |
| 49 | 1456 | June-Reg | Will Jostock | P | 18 | 6-6 | 190 | R | R | Rookie | | Pensacola Junior College | |
| 50 | 1483 | June-Reg | Julio Rodriguez | OF | 18 | 6-3 | 185 | R | R | - | | Wabash Valley College | |