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| | 2 | 65 | Dustin Pedroia | $$ | SS | 20 | 8/17/1983 | 5-9 | 180 | R | R | MLB | 2006-2007 | Arizona State University |
| | 3 | 95 | Andrew Dobies | $$ | P | 21 | 4/20/1983 | 6-1 | 190 | L | L | AA | | University of Virginia |
| | 4 | 125 | Tommy Hottovy | | P | 22 | 7/9/1981 | 6-1 | 195 | L | L | AA | | Wichita State University |
| | 5 | 155 | Ryan Schroyer | | P | 22 | 9/28/1981 | 6-1 | 215 | R | R | AAA | | San Diego State University |
| | 6 | 185 | Cla Meredith | | P | 21 | 6/4/1983 | 6-0 | 180 | R | R | MLB | 2005-2007 | Virginia Commonwealth University |
| | 7 | 215 | Pat Perry | | C | 21 | 10/3/1982 | 6-1 | 190 | L | R | AA | | University of Northern Colorado |
| | 8 | 245 | Kyle Bono | | P | 21 | 6/29/1983 | 6-2 | 200 | R | R | A+ | | University of Central Florida |
| | 9 | 275 | Matt Vanderbosch | | OF | 22 | 4/12/1982 | 5-8 | 190 | L | L | AAA | | Oral Roberts University |
| | 10 | 305 | Steve Pearce | | 1B | 21 | 4/13/1983 | 5-11 | 209 | R | R | MLB | 2007-2007 | University of South Carolina |
| | 11 | 335 | Ryan Phillips | | P | 20 | 5/29/1984 | 6-4 | 210 | L | L | AA | | Barton County Community College |
| | 12 | 365 | Mike Rozier | | P | 18 | 7/4/1985 | 6-5 | 210 | L | L | AA | | Henry County High School (McDonough,GA) |
| | 13 | 395 | Matt Ciaramella | | OF | 21 | 10/25/1982 | 6-1 | 190 | B | L | AA | | University of Utah |
| | 14 | 425 | R.J. Swindle | | P | 20 | 7/7/1983 | 6-3 | 195 | L | L | AAA | | Charleston Southern University |
| | 15 | 455 | Dustin Kelly | | SS | 21 | 5/23/1983 | 6-0 | 185 | R | R | AA | | Cuesta College |
| | 16 | 485 | Matt Clarkson | | C | 20 | 2/24/1984 | 6-1 | 190 | L | R | A- | | University of Arkansas-Fort Smith |
| | 17 | 515** | Jeremy Haynes | | OF | 18 | 5/28/1986 | 6-2 | 180 | R | R | A | | Madison County High School (Madison,FL) |
| | 18 | 545 | Randy Beam | | P | 22 | 5/21/1982 | 6-4 | 225 | L | L | AA | | Florida Atlantic University |
| | 19 | 575 | Logan Sorensen | | 1B | 22 | 8/12/1981 | 6-1 | 195 | L | L | AAA | | Wichita State University |
| | 20 | 605 | Brian Van Kirk | | C | | | | | | | College | | Westminster Academy High School (Fort Lauderdale,FL) |
| | 21 | 635 | Chuck Jeroloman | | SS | 21 | 9/14/1982 | 6-1 | 190 | R | R | AAA | | Auburn University |
| | 22 | 665 | Tim Burgess | | 1B | 22 | 11/3/1981 | 6-2 | 205 | L | L | A | | Georgia State University |
| | 23 | 695 | Matt Goodson | | P | 21 | 9/26/1982 | 6-3 | 195 | R | R | AA | | University of Texas |
| | 24 | 725 | Matt Spencer | | 1B | | | | | | | - | | Morristown West High School (Morristown,TN) |
| | 25 | 755 | Michael Jones | | OF | | | | | | | AA | | Arizona Western College |
| | 26 | 785** | Jake Renshaw | | P | 18 | 4/29/1986 | 6-3 | 215 | R | R | A | | Ventura College |
| | 27 | 815** | Justin Phillabaum | | P | 18 | 4/18/1986 | 6-3 | 210 | R | R | Rookie | | Royal Palm Beach High School (West Palm Beach,FL) |
| | 28 | 845 | Michael James | | P | 23 | 6/2/1981 | 6-0 | 190 | R | R | AA | | University of Connecticut |
| | 29 | 875 | David Seccombe | | P | 22 | 1/9/1982 | 6-0 | 180 | R | R | A | | UNLV |
| | 30 | 905 | Drew Ehrlich | | P | 22 | 2/1/1982 | 6-6 | 230 | R | R | AA | | Stanford University |
| | 31 | 935 | Brendan Winn | | OF | | | | 0 | | | College | | University of South Carolina |
| | 32 | 965 | Brad Hertzler | | P | 18 | 4/11/1986 | 6-1 | 210 | R | L | A- | | East Providence High School (East Providence,RI) |
| | 33 | 995 | John Wells | | P | | | | | | | - | | Timber Creek High School (Orlando,FL) |
| | 34 | 1025 | Andrew Pinckney | | 3B | 22 | 4/7/1982 | 6-1 | 195 | B | R | AA | | Emory University |
| | 35 | 1055** | Bo Lanier | | P | 21 | 11/20/1982 | 6-0 | 160 | R | R | A+ | | University of Georgia |
| | 36 | 1085 | Cooper Eddy | | P | 22 | 4/14/1982 | 6-1 | 205 | R | R | A- | | University of New Mexico |
| | 37 | 1115** | Glenn Swanson | | P | 21 | 5/15/1983 | 6-1 | 175 | L | L | A+ | | University of California-Irvine |
| | 38 | 1145 | Colby Summer | | P | | | | 0 | | | College | | University of Hawaii-Manoa |
| | 39 | 1175 | Zak Farkes | | SS | 21 | 5/30/1983 | 5-11 | 190 | R | R | AA | | Harvard University |
| | 40 | 1205 | Nick Francona | | P | | | 6-3 | 135 | L | L | College | | Lawrenceville (Yardley,PA) |
| | 41 | 1235 | Steven Edlefsen | | SS | 19 | 6/27/1985 | 6-2 | 195 | R | R | A- | | Barton County Community College |
| | 42 | 1264** | Kyle Peter | | OF | 18 | 2/4/1986 | 6-2 | 185 | L | R | A- | | Archbishop O'Hara High School (Kansas City,MO) |
| | 43 | 1293 | Tyler Latham | | P | | | | | | | - | | Hewitt-Trussville High School (Trussville,AL) |
| | 44 | 1322 | Beau Mills | | 3B | 17 | 8/15/1986 | 6-3 | 220 | L | R | A+ | | Golden West High School (Visalia,CA) |
| | 45 | 1351 | Adam Campbell | | 3B | | | | | | | - | | University of British Columbia |
| | 46 | 1380 | Tom Caple | | OF | 23 | 8/20/1980 | 6-0 | 185 | R | R | Rookie | | University of San Diego |
| | 47 | 1409 | Austin Easley | | 1B | 22 | 1/15/1982 | 6-2 | 215 | R | R | AA | | University of Florida |
| | 48 | 1437** | Felipe Garcia | | C-1B | 21 | 5/15/1983 | 6-3 | 225 | R | R | A+ | | California State University, Fullerton |
| | 49 | 1465 | Blake Tillett | | P | | | | | | | College | | Brandon High School (Brandon,FL) |
| | 50 | 1493 | Raudel Alfonso | | P | | | | | | | College | | Hialeah High School (Hialeah,FL) |
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