| 2 | 65 | June-Reg | Dustin Pedroia | SS | 20 | 5-9 | 180 | R | R | MLB | 2006-2009 | Arizona State University | $575,000 |
| 3 | 95 | June-Reg | Andrew Dobies | P | 21 | 6-1 | 190 | L | L | AA | | University of Virginia | $400,000 |
| 4 | 125 | June-Reg | Tommy Hottovy | P | 22 | 6-1 | 195 | L | L | AA | | Wichita State University | $110,000 |
| 5 | 155 | June-Reg | Ryan Schroyer | P | 22 | 6-1 | 215 | R | R | AAA | | San Diego State University | $90,000 |
| 6 | 185 | June-Reg | Cla Meredith | P | 21 | 6-0 | 180 | R | R | MLB | 2005-2009 | Virginia Commonwealth University | $135,000 |
| 7 | 215 | June-Reg | Pat Perry | C | 21 | 6-1 | 190 | L | R | AA | | University of Northern Colorado | $95,000 |
| 8 | 245 | June-Reg | Kyle Bono | P | 21 | 6-2 | 200 | R | R | A+ | | University of Central Florida | $432,000 |
| 9 | 275 | June-Reg | Matt Vanderbosch | OF | 22 | 5-8 | 190 | L | L | AAA | | Oral Roberts University | $10,000 |
| 10 | 305** | June-Reg | Steve Pearce | 1B | 21 | 5-11 | 209 | R | R | MLB | 2007-2009 | University of South Carolina | |
| 11 | 335 | June-Reg | Ryan Phillips | P | 20 | 6-4 | 210 | L | L | A | | Barton County Community College | |
| 12 | 365 | June-Reg | Mike Rozier | P | 18 | 6-5 | 210 | L | L | AA | | Henry County (McDonough,GA) | |
| 13 | 395 | June-Reg | Matt Ciaramella | OF | 21 | 6-1 | 190 | B | L | AA | | University of Utah | |
| 14 | 425 | June-Reg | R.J. Swindle | P | 20 | 6-3 | 195 | L | L | MLB | 2008-2009 | Charleston Southern University | |
| 15 | 455 | June-Reg | Dustin Kelly | SS | 21 | 6-0 | 185 | R | R | AA | | Cuesta College | |
| 16 | 485 | June-Reg | Matt Clarkson | C | 20 | 6-1 | 190 | L | R | A- | | University of Arkansas-Fort Smith | |
| 17 | 515** | June-Reg | Jeremy Haynes | OF | 18 | 6-2 | 180 | R | R | A+ | | Madison County (Madison,FL) | |
| 18 | 545 | June-Reg | Randy Beam | P | 22 | 6-4 | 225 | L | L | AA | | Florida Atlantic University | |
| 19 | 575 | June-Reg | Logan Sorensen | 1B | 22 | 6-1 | 195 | L | L | AAA | | Wichita State University | |
| 20 | 605 | June-Reg | Brian Van Kirk | C | 18 | 6-1 | 225 | R | R | AA | | Westminster Academy (Fort Lauderdale,FL) | |
| 21 | 635 | June-Reg | Chuck Jeroloman | SS | 21 | 6-1 | 190 | R | R | AAA | | Auburn University | |
| 22 | 665 | June-Reg | Tim Burgess | 1B | 22 | 6-2 | 205 | L | L | A | | Georgia State University | |
| 23 | 695 | June-Reg | Matt Goodson | P | 21 | 6-3 | 195 | R | R | AA | | University of Texas | |
| 24 | 725 | June-Reg | Travis Tucker | 1B | 17 | 5-10 | 170 | R | R | College | | Morristown West (Morristown,TN) | |
| 25 | 755 | June-Reg | Michael Jones | OF | 19 | 6-3 | 220 | L | R | A+ | | Arizona Western College | |
| 26 | 785** | June-Reg | Jake Renshaw | P | 18 | 6-3 | 215 | R | R | A+ | | Ventura College | |
| 27 | 815** | June-Reg | Justin Phillabaum | P | 18 | 6-3 | 210 | R | R | A+ | | Royal Palm Beach (West Palm Beach,FL) | |
| 28 | 845 | June-Reg | Mike James | P | 23 | 6-0 | 190 | R | R | AA | | University of Connecticut | |
| 29 | 875 | June-Reg | David Seccombe | P | 22 | 6-0 | 180 | R | R | A | | UNLV | |
| 30 | 905 | June-Reg | Drew Ehrlich | P | 22 | 6-6 | 230 | R | R | AA | | Stanford University | |
| 31 | 935 | June-Reg | Brendan Winn | OF | 21 | 6-1 | 193 | R | R | College | | University of South Carolina | |
| 32 | 965 | June-Reg | Brad Hertzler | P | 18 | 6-1 | 210 | R | L | A | | East Providence (East Providence,RI) | |
| 33 | 995 | June-Reg | John Wells | P | | | | | | - | | Timber Creek (Orlando,FL) | |
| 34 | 1025 | June-Reg | Andrew Pinckney | 3B | 22 | 6-1 | 195 | B | R | AA | | Emory University | |
| 35 | 1055** | June-Reg | Bo Lanier | P | 21 | 6-0 | 160 | R | R | A+ | | University of Georgia | |
| 36 | 1085 | June-Reg | Cooper Eddy | P | 22 | 6-1 | 205 | R | R | A- | | University of New Mexico | |
| 37 | 1115** | June-Reg | Glenn Swanson | P | 21 | 6-1 | 175 | L | L | A+ | | University of California-Irvine | |
| 38 | 1145 | June-Reg | Colby Summer | P | | | 0 | | | College | | University of Hawaii | |
| 39 | 1175 | June-Reg | Zak Farkes | SS | 21 | 5-11 | 210 | R | R | A+ | | Harvard University | |
| 40 | 1205 | June-Reg | Nick Francona | P | | 6-3 | 135 | L | L | College | | Lawrenceville (Yardley,PA) | |
| 41 | 1235 | June-Reg | Steve Edlefsen | SS | 19 | 6-2 | 195 | R | R | AAA | | Barton County Community College | |
| 42 | 1264** | June-Reg | Kyle Peter | OF | 18 | 6-2 | 185 | L | R | A+ | | Archbishop O'Hara (Kansas City,MO) | |
| 43 | 1293 | June-Reg | Tyler Latham | P | | | | | | - | | Hewitt-Trussville (Trussville,AL) | |
| 44 | 1322 | June-Reg | Beau Mills | 3B | 17 | 6-3 | 220 | L | R | AA | | Golden West (Visalia,CA) | |
| 45 | 1351 | June-Reg | Adam Campbell | 3B | | | | | | - | | University of British Columbia | |
| 46 | 1380 | June-Reg | Tom Caple | OF | 23 | 6-0 | 185 | R | R | Rookie | | University of San Diego | |
| 47 | 1409 | June-Reg | Austin Easley | 1B | 22 | 6-2 | 215 | R | R | AA | | University of Florida | |
| 48 | 1437** | June-Reg | Felipe Garcia | C-1B | 21 | 6-3 | 225 | R | R | A+ | | Cal State Fullerton | |
| 49 | 1465 | June-Reg | Blake Tillett | P | | | | | | College | | Brandon (Brandon,FL) | |
| 50 | 1493 | June-Reg | Raudel Alfonso | P | | | | | | College | | Hialeah (Hialeah,FL) | |