| 1 | 7 | June-Reg | Nick Markakis | OF | 19 | 6-2 | 195 | L | L | MLB | 2006-2009 | Young Harris College | $1,850,000 |
| 2 | 44 | June-Reg | Brian Finch | P | 21 | 6-4 | 195 | R | R | AA | | Texas A&M University | $750,000 |
| 3 | 74 | June-Reg | Chris Ray | P | 21 | 6-2 | 190 | R | R | MLB | 2005-2009 | College of William and Mary | $485,000 |
| 4 | 104 | June-Reg | Bob McCrory | P | 21 | 6-0 | 205 | R | R | MLB | 2008-2009 | University of Southern Mississippi | $300,000 |
| 5 | 134 | June-Reg | Nate Spears | SS | 18 | 5-11 | 168 | L | R | AAA | | Charlotte (Punta Gorda,FL) | $215,000 |
| 6 | 164 | June-Reg | Eric Sultemeier | OF | 21 | 6-2 | 195 | R | R | A | | University of Texas | $150,000 |
| 7 | 194 | June-Reg | Justin Azze | P | 20 | 6-3 | 205 | L | L | A- | | University of Hawaii | $110,000 |
| 8 | 224** | June-Reg | Nathan Nery | P | 17 | 6-4 | 212 | R | L | A+ | | Moon Area (Coraopolis,PA) | |
| 9 | 254 | June-Reg | Jarod Rine | OF | 21 | 6-0 | 190 | L | R | A+ | | West Virginia University | $70,000 |
| 10 | 284 | June-Reg | Jacob Duncan | OF | 21 | 5-11 | 195 | L | L | A+ | | Texas Christian University | $50,000 |
| 11 | 314 | June-Reg | Matt Houston | C | 21 | 5-11 | 200 | R | R | A+ | | Oklahoma City University | |
| 12 | 344 | June-Reg | Matt Pulley | 3B | 18 | 6-3 | 200 | L | R | AA | | Woodland (Woodland,CA) | |
| 13 | 374 | June-Reg | James Hoey | P | 20 | 6-6 | 200 | R | R | MLB | 2006-2007 | Rider University | |
| 14 | 404 | June-Reg | Brian Bock | C | 21 | 6-0 | 205 | R | R | AAA | | University of Hawaii | |
| 15 | 434** | June-Reg | Jordan Timm | P | 22 | 6-6 | 230 | L | L | A+ | | University of Wisconsin-Oshkosh | |
| 16 | 464 | June-Reg | Alan Beck | OF | 22 | 6-1 | 220 | R | R | A- | | Western Carolina University | |
| 17 | 494 | June-Reg | Lorenzo Scott | OF | 21 | 6-3 | 210 | L | L | AAA | | Ball State University | |
| 18 | 524 | June-Reg | Jason Furrow | P | 18 | 6-4 | 185 | R | L | Ind | | Judson (Converse,TX) | |
| 19 | 554** | June-Reg | Matt Tolbert | 2B | 21 | 6-0 | 177 | B | R | MLB | 2008-2009 | University of Mississippi | |
| 20 | 584 | June-Reg | Tony Neal | P | 22 | 6-2 | 205 | R | R | A+ | | University of South Alabama | |
| 21 | 614 | June-Reg | David Cash | SS | 17 | 6-3 | 180 | B | R | A+ | | Northside Christian (St. Petersburg,FL) | |
| 22 | 644 | June-Reg | Zachary Dixon | P | 22 | 6-2 | 195 | L | L | A+ | | Texas A&M University | |
| 23 | 674 | June-Reg | Dennis Wyrick | 3B | 22 | 6-1 | 215 | R | R | A- | | Arizona State University | |
| 24 | 704 | June-Reg | Josh McCurdy | OF | 23 | 6-6 | 215 | R | R | AAA | | Niagara University | |
| 25 | 734 | June-Reg | Richard Hummel | OF | 18 | 6-0 | 160 | B | R | Rookie | | Tombstone (Tombstone,AZ) | |
| 26 | 764 | June-Reg | Brian LeClerc | OF | 18 | 5-10 | 175 | L | R | A | | Northside Christian (St. Petersburg,FL) | |
| 27 | 794 | June-Reg | Travis Brown | SS | 22 | 6-0 | 180 | R | R | AAA | | Western Kentucky University | |
| 28 | 824 | June-Reg | Russell Brocato | P | 20 | 6-3 | 190 | R | R | A- | | University of Pennsylvania | |
| 29 | 854 | June-Reg | Jason Ward | P | 21 | 6-3 | 190 | R | R | College | | Utah Valley State College | |
| 30 | 884 | June-Reg | Chris Osentowski | P | 23 | 6-2 | 180 | R | R | College | | Texas Christian University | |
| 31 | 914 | June-Reg | Ryan Brnardic | P | 21 | 6-4 | 215 | L | R | Ind | | Southeastern Oklahoma State University | |
| 32 | 944 | June-Reg | Landon Wareham | 2B | 22 | 5-11 | 180 | R | R | A- | | Mesa State College | |
| 33 | 974 | June-Reg | Jake Muyco | C | 18 | 6-1 | 170 | R | R | AA | | Columbia Basin College | |
| 34 | 1004 | June-Reg | Brad Wiggins | OF | 19 | 6-0 | 180 | B | R | A- | | Howard College | |
| 35 | 1034 | June-Reg | Richard Orange | OF | 18 | 6-2 | 200 | R | R | - | | Greenville (Greenville,TX) | |
| 36 | 1064 | June-Reg | Danny Martin | OF | 18 | 6-1 | 185 | R | R | - | | Dunedin (Dunedin,FL) | |
| 37 | 1094 | June-Reg | David Smith | P | 19 | 6-5 | 195 | R | R | - | | New Castle Chrysler (New Castle,IN) | |
| 38 | 1124** | June-Reg | Matthew Garnett | P | 18 | 6-7 | 220 | L | L | - | | Stockdale (Bakersfield,CA) | |
| 39 | 1154 | June-Reg | Shaun Corning | P | 19 | 6-0 | 180 | L | L | College | | Madison Area Technical College | |
| 40 | 1184** | June-Reg | Joe Welsh | P | 18 | 6-4 | 180 | L | L | A | | Grand Rapids Community College | |
| 41 | 1214 | June-Reg | Aaron Feterl | P | 18 | 6-2 | 170 | R | R | - | | Crescenta Valley (La Crescenta,CA) | |
| 42 | 1243 | June-Reg | Chad Boudon | OF | 22 | 6-1 | 215 | R | R | A- | | University of Washington | |
| 43 | 1272 | June-Reg | Kyle George | SS | 21 | 6-0 | 195 | R | R | Ind | | University of Maryland | |
| 44 | 1300 | June-Reg | Scott Houin | OF | 18 | 6-1 | 180 | R | R | A+ | | Rampart (Colorado Springs,CO) | |
| 45 | 1328 | June-Reg | Brett Jensen | P | 19 | 6-7 | 180 | R | R | AA | | Iowa Central Community College | |
| 46 | 1355** | June-Reg | Gregory Young | OF | 18 | 6-2 | 190 | R | R | - | | Old Mill (Millersville,MD) | |
| 47 | 1382 | June-Reg | Roy Irle | P | 20 | 6-5 | 225 | R | R | Ind | | Rend Lake College | |
| 48 | 1409 | June-Reg | Cameron McGuire | C | 19 | 6-3 | 205 | R | R | Ind | | McLennan Community College | |
| 49 | 1435** | June-Reg | Casey Janssen | P | 21 | 6-3 | 190 | R | R | MLB | 2006-2009 | UCLA | |
| 50 | 1461 | June-Reg | Adam Ricciardulli | OF | 18 | 6-2 | 190 | R | R | - | | Mission Bay (San Diego,CA) | |