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| | 1 | 7 | Nick Markakis | $$ | OF | 19 | 11/17/1983 | 6-1 | 170 | L | L | MLB | 2006-2007 | Young Harris College |
| | 2 | 44 | Brian Finch | $$ | P | 21 | 9/27/1981 | 6-4 | 195 | R | R | AA | | Texas A&M University |
| | 3 | 74 | Chris Ray | $$ | P | 21 | 1/12/1982 | 6-2 | 190 | R | R | MLB | 2005-2007 | College of William and Mary |
| | 4 | 104 | Bob McCrory | | P | 21 | 5/3/1982 | 6-0 | 205 | R | R | AA | | University of Southern Mississippi |
| | 5 | 134 | Nate Spears | | SS | 18 | 5/3/1985 | 5-11 | 155 | L | R | AA | | Charlotte High School (Punta Gorda,FL) |
| | 6 | 164 | Eric Sultemeier | | OF | 21 | 6/28/1982 | 6-2 | 195 | R | R | A | | University of Texas |
| | 7 | 194 | Justin Azze | | P | 20 | 9/14/1982 | 6-3 | 205 | L | L | A- | | University of Hawaii-Manoa |
| | 8 | 224** | Nathan Nery | | P | 17 | 8/25/1985 | 6-4 | 212 | R | L | A- | | Moon Area High School (Coraopolis,PA) |
| | 9 | 254 | Jarod Rine | | OF | 21 | 11/14/1981 | 6-0 | 190 | L | R | A+ | | West Virginia University |
| | 10 | 284 | Jacob Duncan | | OF | 21 | 11/20/1981 | 5-11 | 195 | L | L | A+ | | Texas Christian University |
| | 11 | 314 | Matt Houston | | C | 21 | 2/1/1982 | 5-11 | 200 | R | R | A+ | | Oklahoma City University |
| | 12 | 344 | Matt Pulley | | 3B | 18 | 5/15/1985 | 6-3 | 200 | L | R | AA | | Woodland High School (Woodland,CA) |
| | 13 | 374 | James Hoey | | P | 20 | 12/30/1982 | 6-6 | 200 | R | R | MLB | 2006-2007 | Rider University |
| | 14 | 404 | Brian Bock | | C | 21 | 8/24/1981 | 6-0 | 205 | R | R | AAA | | University of Hawaii-Manoa |
| | 15 | 434** | Jordan Timm | | P | 22 | 1/15/1981 | 6-6 | 230 | L | L | A+ | | University of Wisconsin, Oshkosh |
| | 16 | 464 | Alan Beck | | OF | 22 | 10/5/1980 | 6-1 | 220 | R | R | A- | | Western Carolina University |
| | 17 | 494 | Lorenzo Scott | | OF | 21 | 3/1/1982 | 6-3 | 210 | L | L | A+ | | Ball State University |
| | 18 | 524 | Jason Furrow | | P | 18 | 12/31/1984 | 6-4 | 185 | R | L | Ind | | Judson High School (Converse,TX) |
| | 19 | 554** | Matt Tolbert | | 2B | 21 | 5/4/1982 | 6-0 | 177 | B | R | AAA | | University of Mississippi |
| | 20 | 584 | Tony Neal | | P | 22 | 9/12/1980 | 6-2 | 205 | R | R | A+ | | University of South Alabama |
| | 21 | 614 | David Cash | | SS | 17 | 11/22/1985 | 6-3 | 180 | B | R | A | | Northside Christian High School (St. Petersburg,FL) |
| | 22 | 644 | Zachary Dixon | | P | 22 | 11/29/1980 | 6-2 | 195 | L | L | A+ | | Texas A&M University |
| | 23 | 674 | Dennis Wyrick | | 3B | 22 | 2/9/1981 | 6-1 | 215 | R | R | A- | | Arizona State University |
| | 24 | 704 | Josh McCurdy | | OF | 23 | 12/28/1979 | 6-6 | 215 | R | R | AAA | | Niagara University |
| | 25 | 734 | Richard Hummel | | OF | 18 | 5/15/1985 | 6-0 | 160 | B | R | Rookie | | Tombstone High School (Tombstone,AZ) |
| | 26 | 764 | Brian LeClerc | | OF | 18 | 1/12/1985 | 5-10 | 175 | L | R | A | | Northside Christian High School (St. Petersburg,FL) |
| | 27 | 794 | Travis Brown | | SS | 22 | 8/1/1980 | 6-0 | 180 | R | R | AAA | | Western Kentucky University |
| | 28 | 824 | Russell Brocato | | P | 20 | 11/9/1982 | 6-3 | 190 | R | R | A- | | University of Pennsylvania |
| | 29 | 854 | Jason Ward | | P | 21 | 6/7/1982 | 6-3 | 190 | R | R | College | | Utah Valley State College |
| | 30 | 884 | Chris Osentowski | | P | 23 | 3/11/1980 | 6-2 | 180 | R | R | A- | | Texas Christian University |
| | 31 | 914 | Ryan Brnardic | | P | 21 | 11/4/1981 | 6-4 | 215 | L | R | Ind | | Southeastern Oklahoma State University |
| | 32 | 944 | Landon Wareham | | 2B | 22 | 9/21/1980 | 5-11 | 180 | R | R | A- | | Mesa State College |
| | 33 | 974 | Jake Muyco | | C | 18 | 9/16/1984 | 6-1 | 170 | R | R | A+ | | Columbia Basin College |
| | 34 | 1004 | Brad Wiggins | | OF | 19 | 7/9/1983 | 6-0 | 180 | B | R | A- | | Howard College |
| | 35 | 1034 | Richard Orange | | OF | 18 | 10/24/1984 | 6-2 | 200 | R | R | - | | Greenville High School (Greenville,TX) |
| | 36 | 1064 | Danny Martin | | OF | 18 | 1/21/1985 | 6-1 | 185 | R | R | - | | Dunedin High School (Dunedin,FL) |
| | 37 | 1094 | David Smith | | P | 19 | 6/5/1984 | 6-5 | 195 | R | R | - | | New Castle Chrysler High School (New Castle,IN) |
| | 38 | 1124** | Matthew Garnett | | P | 18 | 12/26/1984 | 6-7 | 220 | L | L | - | | Stockdale High School (Bakersfield,CA) |
| | 39 | 1154 | Shaun Corning | | P | 19 | 7/2/1983 | 6-0 | 180 | L | L | College | | Madison Area Technical College |
| | 40 | 1184** | Joe Welsh | | P | 18 | 9/29/1984 | 6-4 | 180 | L | L | A | | Grand Rapids Community College |
| | 41 | 1214 | Aaron Feterl | | P | 18 | 10/29/1984 | 6-2 | 170 | R | R | - | | Crescenta Valley High School (La Crescenta,CA) |
| | 42 | 1243 | Chad Boudon | | OF | 22 | 6/9/1981 | 6-1 | 215 | R | R | A- | | University of Washington |
| | 43 | 1272 | Kyle George | | SS | 21 | 10/14/1981 | 6-0 | 195 | R | R | Ind | | University of Maryland |
| | 44 | 1300 | Scott Houin | | OF | 18 | 4/11/1985 | 6-1 | 180 | R | R | Rookie | | Rampart High School (Colorado Springs,CO) |
| | 45 | 1328 | Brett Jensen | | P | 19 | 11/29/1983 | 6-7 | 180 | R | R | A | | Iowa Central Community College |
| | 46 | 1355** | Gregory Young | | OF | 18 | 3/11/1985 | 6-2 | 190 | R | R | - | | Old Mill High School (Millersville,MD) |
| | 47 | 1382 | Roy Irle | | P | 20 | 10/16/1982 | 6-5 | 225 | R | R | College | | Rend Lake College |
| | 48 | 1409 | Cameron McGuire | | C | 19 | 9/29/1983 | 6-3 | 205 | R | R | Ind | | McLennan Community College |
| | 49 | 1435** | Casey Janssen | | P | 21 | 9/17/1981 | 6-3 | 190 | R | R | MLB | 2006-2007 | UCLA |
| | 50 | 1461 | Adam Ricciardulli | | OF | 18 | 2/21/1985 | 6-2 | 190 | R | R | - | | Mission Bay High School (San Diego,CA) |
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