| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 2 | 60 | June-Reg | Garrett Berger | $$ | P | 18 | 5/11/1983 | 6-3 | 240 | R | R | Ind | | Carmel High School (Carmel,IN) |
| 3 | 92 | June-Reg | Allen Baxter | $$ | P | 17 | 7/6/1983 | 6-4 | 215 | R | R | A+ | | Varina High School (Richmond,VA) |
| 4 | 122 | June-Reg | Chris Resop | | OF | 18 | 11/4/1982 | 6-3 | 200 | R | R | MLB | 2005-2008 | Barron Collier High School (Naples,FL) |
| 5 | 152** | June-Reg | Tyler Lumsden | | P | 18 | 5/9/1983 | 6-4 | 200 | R | L | AAA | | Cave Spring High School (Roanoke,VA) |
| 6 | 182 | June-Reg | Adam Bostick | | P | 18 | 3/17/1983 | 6-1 | 220 | L | L | AAA | | Greensburg-Salem High School (Greensburg,PA) |
| 7 | 212 | June-Reg | Lincoln Holdzkom | | P | 19 | 3/23/1982 | 6-4 | 240 | R | R | AAA | | Arizona Western College |
| 8 | 242 | June-Reg | Jeff Fulchino | | P | 21 | 11/26/1979 | 6-5 | 240 | R | R | MLB | 2006-2008 | University of Connecticut |
| 9 | 272 | June-Reg | Dustin Kupper | | P | 20 | 2/22/1981 | 6-6 | 190 | R | R | A- | | Pima Community College |
| 10 | 302 | June-Reg | Kody Naylor | | P | 21 | 3/8/1980 | 6-2 | 200 | R | R | A- | | Western Michigan University |
| 11 | 332 | June-Reg | Rex Rundgren | | IF | 20 | 11/20/1980 | 6-1 | 170 | R | R | AAA | | Sacramento City College |
| 12 | 362 | June-Reg | Nic Ungs | | P | 21 | 9/3/1979 | 6-1 | 220 | R | R | AAA | | University of Northern Iowa |
| 13 | 392 | June-Reg | Lance Davis | | P | 19 | 11/19/1981 | 6-2 | 190 | R | R | A- | | George County High School (Lucedale,MS) |
| 14 | 422 | June-Reg | Michael Tucker | | IF | 21 | 11/7/1979 | 6-3 | 200 | R | R | AA | | Florida Southern College |
| 15 | 452** | June-Reg | Doug Boone | | C | 22 | 5/16/1979 | 6-1 | 200 | R | R | AA | | Ball State University |
| 16 | 482 | June-Reg | Hunter Wyant | | IF | 22 | 10/4/1978 | 6-2 | 195 | R | R | A | | University of Virginia |
| 17 | 512 | June-Reg | Kevin Cave | | P | 21 | 5/25/1980 | 6-3 | 215 | R | R | AA | | Xavier University |
| 18 | 542 | June-Reg | Josh Coffey | | C | 17 | 8/4/1983 | 6-2 | 180 | R | R | Rookie | | Lee-Davis High School (Mechanicsville,VA) |
| 19 | 572 | June-Reg | Louis Evans | | P | 20 | 10/5/1980 | 6-5 | 213 | L | L | A+ | | San Jose City College |
| 20 | 602 | June-Reg | Will Lafferty | | C | 22 | 4/18/1979 | 6-2 | 200 | R | R | A+ | | University of Mississippi |
| 21 | 632** | June-Reg | Dane Mason | | P | 18 | 12/3/1982 | 6-0 | 175 | R | R | Rookie | | Cherokee High School (Marlton,NJ) |
| 22 | 662 | June-Reg | Jason Helps | | SS | 22 | 12/20/1978 | 6-0 | 180 | B | R | A+ | | Central Michigan University |
| 23 | 692 | June-Reg | Wes Mccrotty | | P | 22 | 6/22/1979 | 6-1 | 190 | L | L | A | | University of Arkansas |
| 24 | 722 | June-Reg | John Skinner | | P | 24 | 6/15/1977 | 6-1 | 185 | R | R | AA | | San Diego State University |
| 25 | 752 | June-Reg | Philip Hartig | | 1B | 23 | 12/18/1977 | 6-3 | 210 | R | R | A | | The Citadel |
| 26 | 782** | June-Reg | Adam Russell | | | 18 | 4/14/1983 | 6-8 | 250 | R | R | AA | | North Olmsted High School (North Olmsted,OH) |
| 27 | 812 | June-Reg | Franco Blackburn | | OF | 22 | 2/18/1979 | 6-1 | 185 | R | L | A | | Southern University |
| 28 | 842** | June-Reg | Jonathan Hunton | | P | 18 | 11/30/1982 | 6-9 | 230 | R | R | A+ | | North Plainfield High School (North Plainfield,NJ) |
| 29 | 872 | June-Reg | Gooby Gerlits | | C | 18 | 11/17/1982 | 6-0 | 200 | R | R | A- | | Stoneman Douglas High School (Parkland,FL) |
| 30 | 902** | June-Reg | Nick Pesco | | P | 17 | 9/17/1983 | 6-6 | 200 | R | R | AAA | | Tokay High School (Lodi,CA) |
| 31 | 932 | June-Reg | Chris Johnston | | P | | | | 0 | | | - | | Smoky Hill High School (Aurora,CO) |
| 32 | 962** | June-Reg | Sergio Roman | | C | | | | 0 | | | - | | Bishop Carroll High School (Wichita,KS) |
| 33 | 992 | June-Reg | Torik Harrison | | P | 21 | 9/10/1979 | 5-11 | 190 | R | R | Ind | | Southern University |
| 34 | 1022 | June-Reg | Steve Thomas | | | | | | | | | A- | | Nova Southeastern University |
| 35 | 1052 | June-Reg | Marc Rittenhouse | | | 22 | 6/9/1979 | 5-10 | 180 | R | R | A- | | University of Washington |
| 36 | 1082 | June-Reg | Kevin Halamicek | | P | 23 | 10/23/1977 | 6-1 | 190 | R | R | A | | California State University, Dominguez Hills |
| 37 | 1112 | June-Reg | Kris Clute | | IF | 22 | 4/20/1979 | 5-9 | 175 | R | R | AA | | University of Miami (Florida) |
| 38 | 1142 | June-Reg | Ronnie Goodwin | | | 21 | 8/30/1979 | 6-1 | 175 | R | R | A- | | University of Mississippi |
| 39 | 1172 | June-Reg | Justin Ottman | | | 19 | 12/1/1981 | 6-5 | 205 | L | L | Ind | | Rockland Community College |
| 40 | 1202 | June-Reg | Tyson Graham | | OF | 18 | 1/12/1983 | 6-3 | 210 | R | R | Rookie | | North Gaston High School (Gastonia,NC) |
| 41 | 1231 | June-Reg | Eric Otero | | 2B | | | 6-0 | 220 | R | R | - | | Monsignor Pace High School (Miami,FL) |
| 42 | 1259 | June-Reg | Josh Perrault | | | 19 | 6/11/1982 | 6-3 | 205 | R | R | AAA | | South Mountain Community College |
| 43 | 1287 | June-Reg | Isaac Garza | | P | 17 | 8/3/1983 | 6-3 | 205 | R | R | - | | Odem High School (Odem,TX) |
| 44 | 1315 | June-Reg | Cliff Dancy | | OF | 21 | 2/7/1980 | 6-1 | 185 | R | R | A | | Pine Forest High School (Pensacola,FL) |
| 45 | 1343** | June-Reg | Nick Blasi | | | 19 | 9/23/1981 | 5-9 | 185 | R | R | AAA | | Butler County Community College |
| 46 | 1371 | June-Reg | Andrew Vansickle | | RF | | | | 0 | | | - | | Senatobia High School (Senatobia,MS) |
| 47 | 1398 | June-Reg | Chuck Taylor | | P | 59 | 4/18/1942 | 6-2 | 195 | R | R | MLB | 1969-1976 | Westlake High School (Austin,TX) |
| 48 | 1425 | June-Reg | Derek Hutton | | | | | | | | | College | | Palm Beach Gardens High School (Palm Beach Gardens,FL) |
| 49 | 1450** | June-Reg | Phillip Coke | | P | 18 | 7/19/1982 | 6-1 | 210 | L | L | AAA | | Sonora High School (Sonora,CA) |
| 50 | 1473** | June-Reg | Steve Stanley | | OF | 21 | 12/23/1979 | 5-8 | 155 | L | L | AAA | - | University of Notre Dame |
| |