| 1 | 16 | June-Reg | Kip Wells | P | 21 | 6-3 | 196 | R | R | MLB | 1999-2009 | Baylor University | $1,170,000 |
| 1 | 35 | June-Reg | Aaron Rowand | OF | 20 | 6-1 | 200 | R | R | MLB | 2001-2009 | Cal State Fullerton | $575,000 |
| 2 | 59 | June-Reg | Gary Majewski | P | 18 | 6-2 | 200 | R | R | MLB | 2004-2008 | St. Pius X (Houston,TX) | |
| 3 | 89 | June-Reg | Josh Fogg | P | 21 | 6-2 | 205 | R | R | MLB | 2001-2009 | University of Florida | |
| 3 | 102 | June-Reg | Dan Mozingo | P | 18 | 6-2 | 210 | L | L | A+ | | Ashtabula (Ashtabula,OH) | |
| 4 | 119 | June-Reg | Juan Santamarina | IF | 18 | 6-1 | 180 | L | R | A+ | | Gulliver Prep (Coral Gables,FL) | |
| 5 | 149** | June-Reg | Steve Kelly | P | 18 | 6-1 | 195 | R | R | AAA | | Fairfield H.S. (Fairfield H.S.) | |
| 6 | 179 | June-Reg | Matt Borne | P | 21 | 6-3 | 190 | R | R | A+ | | University of Kentucky | |
| 7 | 209 | June-Reg | Eric Fischer | P | 18 | 6-7 | 200 | B | L | A+ | | Moeller (Cincinnati,OH) | |
| 8 | 239 | June-Reg | Mitch Wylie | P | 21 | 6-3 | 190 | R | R | AAA | | St. Ambrose University | |
| 9 | 269 | June-Reg | Gus Mosley | OF | 18 | 6-2 | 185 | R | R | Rookie | | Wakulla (Crawfordville,FL) | |
| 10 | 299** | June-Reg | Steve Bess | IF | 21 | 6-4 | 225 | R | R | AA | | Rice University | |
| 11 | 329 | June-Reg | Mike Williams | P | 19 | 6-3 | 190 | R | R | AAA | | Galveston College | |
| 12 | 359 | June-Reg | Kai Freeman | P | 21 | 6-2 | 182 | R | R | AAA | | University of Minnesota | |
| 13 | 389 | June-Reg | Gerard McCall | C | 18 | 6-0 | 210 | R | R | Ind | | Meridian (Meridian,MS) | |
| 14 | 419** | June-Reg | Solomon Johnson | P | | | 0 | | | - | | Navarro College | |
| 15 | 449** | June-Reg | Nate Robertson | P | 20 | 6-2 | 215 | L | R | MLB | 2002-2009 | Wichita State University | |
| 16 | 479 | June-Reg | Ernesto Lowe | OF | 19 | 6-1 | 180 | R | R | Rookie | | American (Hialeah,FL) | |
| 17 | 509 | June-Reg | Brannon Whatley | P | 21 | 6-1 | 170 | R | R | A+ | | Kennesaw State University | |
| 18 | 539** | June-Reg | Chris Hamblen | C | 18 | 6-1 | 190 | B | R | A+ | | Highlands (Fort Thomas,KY) | |
| 19 | 569 | June-Reg | Jason Stovall | P | | | 0 | | | - | | Battiest (Battiest,OK) | |
| 20 | 599** | June-Reg | Erik Lohse | P | 18 | 6-1 | 205 | R | R | AA | | Hamilton College | |
| 21 | 629 | June-Reg | Andre Simpson | P | 17 | 6-3 | 180 | R | R | A+ | | Mount Miguel (Spring Valley,CA) | |
| 22 | 659 | June-Reg | Carlos Castillo | IF | 18 | 5-10 | 170 | B | R | AA | | Miami-Dade College | |
| 23 | 689** | June-Reg | Todd Johannes | | 21 | 6-3 | 185 | R | R | AAA | | University of Florida | |
| 24 | 719 | June-Reg | Caleb Reger | | | | | | | College | | Bradshaw Mountain (Prescott Valley,AZ) | |
| 25 | 749 | June-Reg | Mark Cochrane | C | 18 | 6-0 | 185 | R | R | A | | Stoneman Douglas (Parkland,FL) | |
| 26 | 779 | June-Reg | Edwin Almonte | P | 21 | 6-2 | 180 | R | R | MLB | 2003-2003 | University of St. Francis | |
| 27 | 809 | June-Reg | Eric Battersby | 1B | 22 | 6-1 | 205 | R | L | AAA | | St. Mary's University | |
| 28 | 839** | June-Reg | Travis Edwards | CF | | | 0 | | | - | | Wilson (Long Beach,CA) | |
| 29 | 869** | June-Reg | Nelson Lopez | P | 17 | 6-2 | 205 | R | R | A | | Monsignor Pace (Miami,FL) | |
| 30 | 899 | June-Reg | Jason Abreu | SS | | | 0 | | | - | | Hialeah (Hialeah,FL) | |
| 31 | 929 | June-Reg | Carlos Cline | 1B | 20 | 6-2 | 210 | L | L | Rookie | | Brookdale Community College | |
| 32 | 959 | June-Reg | Todd Eames | P | | | 0 | R | R | Rookie | | - | |
| 33 | 989 | June-Reg | Paul Reuer | | | | | | | College | | Schaumburg (Schaumburg,IL) | |
| 34 | 1019 | June-Reg | Damione Merriman | OF | | | 0 | | | - | | Averett University | |
| 35 | 1049 | June-Reg | Scott Atwood | 1B | | | 0 | | | - | | University of North Florida | |
| 36 | 1079 | June-Reg | Dan Wells | C | 18 | 6-2 | 210 | R | R | Ind | | Columbine (Littleton,CO) | |
| 37 | 1109** | June-Reg | Jay Bernard | P | 19 | 6-5 | 220 | R | R | A | | Gulf Coast Community College | |
| 38 | 1139 | June-Reg | Mark Buehrle | P | 19 | 6-2 | 200 | L | L | MLB | 2000-2009 | Jefferson Co. (St. Charles,MO) | $150,000 |
| 39 | 1169** | June-Reg | Curtis Young | P | 18 | 6-2 | 170 | R | R | A | | Grand Junction (Grand Junction,CO) | |
| 40 | 1199 | June-Reg | Michael Baetzel | SS | | | 0 | | | Rookie | | Kishwaukee College | |
| 41 | 1229 | June-Reg | Mike Mallonee | P | | | 0 | | | Ind | | Southwestern University | |
| 42 | 1259** | June-Reg | Kevin Cameron | P | 18 | 6-1 | 181 | R | R | MLB | 2007-2009 | Catholic Academy (Joliet,IL) | |
| 43 | 1287 | June-Reg | Mike Scioletti | 3B | | | 0 | | | - | | US Military Academy | |
| 44 | 1313 | June-Reg | Julio Guerrero | OF | 18 | 5-11 | 175 | R | R | College | | San Angelo (San Angelo,TX) | |
| 45 | 1337 | June-Reg | John Gusich | | 18 | 6-3 | 210 | B | R | College | | Deer Valley (Glendale,AZ) | |
| 46 | 1360** | June-Reg | Vince Serafini | P | 18 | 6-1 | 230 | R | L | A | | Lockport Township (Lockport,IL) | |
| 47 | 1382 | June-Reg | Nathan Boyd | | | | | | | College | | Allen Academy (Bryan,TX) | |
| 48 | 1402** | June-Reg | Ryan Costello | P | 18 | 6-6 | 215 | R | L | AA | | Milford Academy (Voorhees,NJ) | |
| 49 | 1419 | June-Reg | Ricardo Suarez | OF | | | 0 | | | - | | Dade Christian School (Miami,FL) | |
| 50 | 1435 | June-Reg | Justin Hairston | 2B | | | 0 | | | - | | College of DuPage | |