| 1 | 23 | June-Reg | Jacoby Ellsbury | of | 21 | 6-1 | 185 | L | L | MLB | 2007-2009 | Oregon State University | $1,400,000 |
| 1 | 26 | June-Reg | Craig Hansen | P | 21 | 6-6 | 210 | R | R | MLB | 2005-2009 | St. John's University | $1,325,000 |
| 1 | 42 | June-Reg | Clay Buchholz | P | 20 | 6-3 | 190 | L | R | MLB | 2007-2009 | Angelina College | $800,000 |
| 1 | 45 | June-Reg | Jed Lowrie | 2b | 21 | 6-0 | 180 | B | R | MLB | 2008-2009 | Stanford University | $762,500 |
| 1 | 47 | June-Reg | Mike Bowden | P | 18 | 6-3 | 215 | R | R | MLB | 2008-2009 | Waubonsie Valley (Aurora,IL) | $730,000 |
| 2 | 57 | June-Reg | Jon Egan | c | 18 | 6-4 | 210 | R | R | A | | Cross Creek (Augusta,GA) | $625,000 |
| 4 | 138 | June-Reg | Scott Blue | P | 18 | 6-2 | 215 | R | R | Rookie | | Morro Bay (Morro Bay,CA) | $75,000 |
| 5 | 168 | June-Reg | Reid Engel | of | 18 | 6-2 | 175 | L | R | AA | | Lewis-Palmer (Monument,CO) | $154,000 |
| 6 | 198 | June-Reg | Jeff Corsaletti | of | 22 | 6-0 | 190 | L | R | AAA | | University of Florida | $50,000 |
| 7 | 228 | June-Reg | Yahmed Yema | OF | 20 | 6-0 | 182 | L | L | A+ | | Florida International University | $90,000 |
| 8 | 258 | June-Reg | J.T. Zink | P | 20 | 6-2 | 195 | R | R | A+ | | Everett Community College | $75,000 |
| 9 | 288 | June-Reg | Mark Wagner | c | 21 | 6-1 | 205 | R | R | AAA | | University of California-Irvine | $90,000 |
| 10 | 318 | June-Reg | Kevin Guyette | P | 22 | 6-3 | 205 | R | R | AAA | | University of Arizona | $50,000 |
| 11 | 348 | June-Reg | Ismael Casillas | P | 22 | 6-3 | 215 | R | R | A+ | | Benedictine College | |
| 12 | 378 | June-Reg | Kyle Fernandes | P | 19 | 6-0 | 185 | L | L | AA | | Massasoit (Massasoit,MA) | |
| 13 | 408 | June-Reg | Jay Johnson | of | 22 | 6-2 | 185 | R | R | AA | | Xavier University | |
| 14 | 438 | June-Reg | Pedro Alvarez | SS | 18 | 6-2 | 225 | L | R | AA | | Horace Mann (Bronx,NY) | |
| 15 | 468** | June-Reg | Patrick Thomas | P | 19 | 5-11 | 190 | L | L | College | | Jeffersonville (Jeffersonville,IN) | |
| 16 | 498 | June-Reg | Matt Mercurio | 3b | 22 | 6-2 | 180 | R | R | A | | Florida Southern College | |
| 17 | 528 | June-Reg | Dominic Ramos | SS | 22 | 5-10 | 180 | R | R | A+ | | Texas State University | |
| 18 | 558 | June-Reg | Nick Criaris | c | 18 | 6-2 | 220 | L | R | College | | | |
| 19 | 588 | June-Reg | Jim Baxter | P | 21 | 6-0 | 195 | L | L | A- | | Villanova University | |
| 20 | 618 | June-Reg | Charles Blackmon | P | 18 | 6-3 | 200 | L | L | A+ | | Young Harris College | |
| 21 | 648 | June-Reg | Solomon Johnson | P | | | 0 | | | - | | Navarro College | |
| 22 | 678 | June-Reg | Orvil Aviles | P | 17 | 6-4 | 0 | L | L | - | | Fernando Callejo (Manati,PR) | |
| 23 | 708 | June-Reg | Carl Lipsey | 2b | 22 | 5-10 | 175 | R | R | A- | | Jackson State University | |
| 24 | 738 | June-Reg | Jason Twomley | OF | 22 | 6-0 | 215 | L | L | AA | | University of Massachusetts | |
| 25 | 768 | June-Reg | Ricardo Sanchez | c | 22 | 5-11 | 215 | R | R | A- | | Barry University | |
| 26 | 798 | June-Reg | Kirby Yates | P | 18 | 5-10 | 170 | L | R | Rookie | | Kauai (Lihue,HI) | |
| 27 | 828 | June-Reg | Matt Hancock | P | 22 | 6-3 | 195 | L | L | A | | Oral Roberts University | |
| 28 | 858 | June-Reg | Ryan Hinson | P | 18 | 6-3 | 220 | L | L | A+ | | Northwestern (Rock Hill,SC) | |
| 29 | 888 | June-Reg | Chris Jones | P | 21 | 6-3 | 205 | R | R | AA | | Indiana State University | |
| 30 | 918 | June-Reg | Ryan Colvin | P | 18 | 6-2 | 170 | R | R | A | | Carroll (Corpus Christi,TX) | |
| 31 | 948 | June-Reg | Luis Exposito | c | 18 | 6-3 | 210 | R | R | AA | | Champagnat Catholic (Hialeah,FL) | |
| 32 | 978 | June-Reg | Jeff Natale | 2B | 22 | 5-9 | 170 | R | R | AAA | | Trinity College | |
| 33 | 1008** | June-Reg | John Hester | c | 21 | 6-4 | 210 | R | R | MLB | 2009-2009 | Stanford University | |
| 34 | 1038** | June-Reg | Allan Dykstra | 1B | 18 | 6-5 | 240 | L | R | A+ | | Rancho Bernardo (San Diego,CA) | $0 |
| 35 | 1068 | June-Reg | Jason Determann | P | 22 | 5-10 | 170 | R | L | College | | Louisiana State University | |
| 36 | 1098 | June-Reg | Mark McClure | P | 18 | 6-8 | 205 | R | R | - | | Hillsborough (Tampa,FL) | |
| 37 | 1128 | June-Reg | Jason Schnitzer | P | 18 | 6-2 | 185 | R | R | - | | Los Alamitos (Los Alamitos,CA) | |
| 38 | 1158 | June-Reg | Levi Tapia | c | 18 | 5-10 | 200 | R | R | Rookie | | Ralston Valley (Arvada,CO) | |
| 39 | 1187 | June-Reg | Bubba Bell | of | 22 | 6-0 | 195 | L | R | AAA | | Nicholls State University | |
| 40 | 1216 | June-Reg | Blake Maxwell | P | 20 | 6-5 | 255 | R | R | AA | | Methodist University | |
| 41 | 1245** | June-Reg | Eddie Degerman | P | 21 | 6-4 | 205 | R | R | AA | | Rice University | |
| 42 | 1274 | June-Reg | Miguel Alicea | OF | 18 | 6-0 | 190 | R | R | AAA | | Manuela Toro (Caguas,PR) | |
| 43 | 1303** | June-Reg | Jason Castro | c | 18 | 6-3 | 210 | L | R | AA | | Castro Valley (Castro Valley,CA) | $0 |
| 44 | 1332 | June-Reg | Chris Garcia | 1b | 17 | 6-1 | 214 | L | R | Rookie | | Xaverian (Brooklyn,NY) | |
| 45 | 1361 | June-Reg | Dustin Bamberg | C | | | | | | College | | Tallahassee Community College | |
| 46 | 1390 | June-Reg | T.J. Large | P | 22 | 6-4 | 185 | R | R | AAA | | University of Alabama | |
| 47 | 1418 | June-Reg | Alex Wolfe | c | 18 | 6-0 | 215 | L | R | - | | Timpanogos (Orem,UT) | |
| 48 | 1446 | June-Reg | Matt Sheely | of | 18 | 5-7 | 165 | R | R | AAA | | Palm Beach Gardens (Palm Beach Gardens,FL) | |
| 49 | 1473 | June-Reg | Erik Turgeon | P | 18 | 6-1 | 185 | R | R | A | | Dunedin (Dunedin,FL) | |
| 50 | 1500 | June-Reg | Colin Arnold | OF | 17 | 6-2 | 185 | L | L | College | | Kings Academy (West Palm Beach,FL) | |