| 1 | 2 | June-Reg | Josh Beckett | P | 19 | 6-4 | 190 | R | R | MLB | 2001-2009 | Spring (Spring,TX) | $3,625,000 |
| 2 | 53 | June-Reg | Terry Byron | P | 20 | 6-0 | 220 | R | R | A+ | | Indian River State College | $350,000 |
| 3 | 86 | June-Reg | Josh Wilson | SS | 18 | 6-0 | 161 | R | R | MLB | 2005-2009 | Mount Lebanon (Pittsburgh,PA) | |
| 4 | 116 | June-Reg | Dominic Woody | C | 20 | 6-3 | 210 | R | R | A+ | | University of Washington | |
| 5 | 146 | June-Reg | Nate Robertson | P | 21 | 6-2 | 215 | L | R | MLB | 2002-2009 | Wichita State University | |
| 6 | 176 | June-Reg | Charles Frazier | OF | 18 | 6-3 | 185 | R | R | AA | | Toms River South (Toms River,NJ) | $300,000 |
| 7 | 206 | June-Reg | Jacob Laidlaw | OF | 17 | 6-2 | 190 | R | R | A- | | Cheyenne (North Las Vegas,NV) | |
| 8 | 236 | June-Reg | Kevin Hooper | IF | 22 | 5-9 | 155 | R | R | MLB | 2005-2006 | Wichita State University | |
| 9 | 266 | June-Reg | Ben Hickman | P | 22 | 6-0 | 240 | R | R | A | | Louisiana Tech University | |
| 10 | 296 | June-Reg | Scott Goodman | LF | 21 | 6-1 | 210 | L | L | A+ | | Arizona State University | |
| 11 | 326 | June-Reg | Randy Messenger | P | 17 | 6-3 | 239 | R | R | MLB | 2005-2009 | Sparks (Sparks,NV) | $327,000 |
| 12 | 356** | June-Reg | Angel Sanchez | 2B | 15 | 6-1 | 170 | R | R | MLB | 2006-2006 | Vineland (Vineland,NJ) | |
| 13 | 386 | June-Reg | Bryan Moore | P | 22 | 6-8 | 215 | R | R | A | | University of Houston | |
| 14 | 416 | June-Reg | Todd Moser | P | 22 | 6-5 | 180 | L | L | AA | | Florida Atlantic University | |
| 15 | 446 | June-Reg | Barry Schell | LF | 21 | 6-2 | 210 | L | L | A- | | Palomar College | |
| 16 | 476 | June-Reg | Jared Wykoff | P | 18 | 6-5 | 190 | R | R | Ind | | Kinder (Kinder,LA) | |
| 17 | 506 | June-Reg | Brad Haynes | P | 17 | 6-5 | 187 | R | R | A+ | | Barren County (Glasgow,KY) | |
| 18 | 536 | June-Reg | Dave Johnston | P | 18 | 6-3 | 190 | R | R | A+ | | Marshalltown (Marshalltown,IA) | |
| 19 | 566 | June-Reg | Kevin Perkins | 2B | 21 | 6-2 | 185 | R | R | A+ | | University of California-Riverside | |
| 20 | 596 | June-Reg | Shane Smuin | P | | 6-2 | 205 | R | R | A+ | | Utah Valley State College | |
| 21 | 626 | June-Reg | Joe Sergent | P | 20 | 6-0 | 185 | L | L | AA | | Lamar University | |
| 22 | 656 | June-Reg | James Close | CF | 21 | 5-10 | 165 | R | R | A+ | | UNLV | |
| 23 | 686** | June-Reg | Jarrod Schmidt | OF | 18 | 6-2 | 200 | R | R | A | | Lassiter (Marietta,GA) | |
| 24 | 716 | June-Reg | Bryan Morse | P | 21 | 5-11 | 160 | L | L | A+ | | Mount Olive College | |
| 25 | 746 | June-Reg | Dennis Anderson | C | 21 | 6-0 | 200 | B | R | AA | | University of Arizona | |
| 26 | 776 | June-Reg | Keith Herbert | SS | | | 0 | | | Rookie | | Boonsboro (Boonsboro,MD) | |
| 27 | 806 | June-Reg | Tom Bell | P | 18 | 6-0 | 185 | R | R | A- | | George C. Marshall (Falls Church,VA) | |
| 28 | 836 | June-Reg | William Ward | P | | | 0 | | | - | | Texas A&M University | |
| 29 | 866 | June-Reg | Matt Postell | C | 22 | 6-4 | 187 | L | R | A | - | North Carolina State University | |
| 30 | 896 | June-Reg | Brandon Bowe | P | 23 | 6-3 | 215 | R | R | AA | | Louisiana State University | |
| 31 | 926 | June-Reg | Kenny Riley | C | 19 | 6-2 | 200 | R | R | A- | | Reed (Sparks,NV) | |
| 32 | 956** | June-Reg | Dustin Griffith | P | 18 | 6-4 | 190 | R | R | AAA | | Dakota Ridge (Littleton,CO) | |
| 33 | 986 | June-Reg | Mike Flannery | P | 19 | 6-1 | 205 | R | R | AAA | | Gloucester County College | |
| 34 | 1016 | June-Reg | John Moylan | C | 19 | | 0 | | | - | | Canada College | |
| 35 | 1046 | June-Reg | Enrique Mendieta | CF | 19 | 6-0 | 175 | R | R | Rookie | | Norfolk State University | |
| 36 | 1076 | June-Reg | Kevin Snowden | CF | | | 0 | | | - | | Roosevelt (Greenbelt,MD) | |
| 37 | 1106 | June-Reg | Derek Caraway | P | | | 0 | | | College | | Andalusia (Andalusia,AL) | |
| 38 | 1136 | June-Reg | Robert Glaser | RF | | | 0 | | | - | | San Joaquin Delta College | |
| 39 | 1166 | June-Reg | Chance Scott | SS | | | 0 | | | - | | Pleasant Grove (Pleasant Grove,UT) | |
| 40 | 1196 | June-Reg | Matt Krabbe | | | | | | | College | | Triton College | |
| 41 | 1226 | June-Reg | Jeff Nichols | | | | | | | College | | Rice University | |
| 42 | 1254** | June-Reg | Adam LaRoche | 1B | 19 | 6-3 | 180 | L | L | MLB | 2004-2009 | Fort Scott Community College | |
| 43 | 1281 | June-Reg | Darin Phalines | P | | | 0 | | | Ind | | Gloucester County College | |
| 44 | 1308 | June-Reg | Alonso Gomez | 3B | | | 0 | | | - | | College of San Mateo | |
| 45 | 1335** | June-Reg | John Anderson | | | | | | | College | | Pine Bluff (Pine Bluff,AR) | |
| 46 | 1360 | June-Reg | Ben Vannatter | | | | | | | College | | Amelia (Amelia,OH) | |
| 47 | 1384 | June-Reg | Jacob Robertson | CF | | | 0 | | | - | | Twin Falls (Twin Falls,ID) | |
| 48 | 1408 | June-Reg | Quian Davis | LF | | | 0 | | | Rookie | | | |
| 49 | 1432 | June-Reg | John Zamora | P | 21 | 6-3 | 220 | R | R | - | | Cabrillo College | |
| 50 | 1455** | June-Reg | Anthony Aceves | CF | | | 0 | | | - | | Howard (Ellicott City,MD) | |