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| | 1 | 20 | Trevor Plouffe | $$ | SS | 18 | 6/15/1986 | 6-1 | 175 | R | R | AA | | Crespi Carmelite High School (Encino,CA) |
| | 1 | 22 | Glen Perkins | $$ | P | 21 | 3/2/1983 | 5-11 | 190 | L | L | MLB | 2006-2007 | University of Minnesota |
| | 1 | 25 | Kyle Waldrop | $$ | P | 18 | 10/27/1985 | 6-4 | 190 | R | R | AA | | Farragut High School (Knoxville,TN) |
| | 1 | 35 | Matt Fox | $$ | P | 21 | 12/4/1982 | 6-3 | 192 | R | R | A | | University of Central Florida |
| | 1 | 39 | Jay Rainville | $$ | P | 18 | 10/16/1985 | 6-3 | 230 | R | R | A+ | | Bishop Hendricken High School (Warwick,RI) |
| | 2 | 61 | Anthony Swarzak | $$ | P | 18 | 9/10/1985 | 6-3 | 195 | R | R | AA | | Nova High School (Davie,FL) |
| | 3 | 91 | Eduardo Morlan | $$ | P | 18 | 3/1/1986 | 6-2 | 210 | R | R | AA | | Coral Park High School (Miami,FL) |
| | 4 | 121 | Mark Robinson | | OF | 18 | 4/7/1986 | 6-1 | 180 | B | R | A | | Mountain View High School (El Monte,CA) |
| | 5 | 151 | Jeff Schoenbachler | | P | 18 | 9/13/1985 | 6-1 | 185 | R | L | Rookie | | Reno High School (Reno,NV) |
| | 6 | 181 | Patrick Bryant | | P | 18 | 10/26/1985 | 6-4 | 190 | R | R | Rookie | | Pensacola Catholic High School (Pensacola,FL) |
| | 7 | 211 | John Williams | | P | 22 | 12/19/1981 | 6-4 | 190 | R | L | A | | Middle Tennessee State University |
| | 8 | 241 | Jay Sawatski | | P | 22 | 5/7/1982 | 6-2 | 195 | L | L | AAA | | University of Arkansas |
| | 9 | 271 | J.P. Martinez | | P | 22 | 6/8/1982 | 6-2 | 205 | R | R | AAA | | University of New Orleans |
| | 10 | 301 | Jeremy Pickrel | | OF | 21 | 4/3/1983 | 6-4 | 225 | L | R | A+ | | Illinois State University |
| | 11 | 331 | Kyle Aselton | | P | 21 | 2/28/1983 | 6-5 | 215 | R | L | A+ | | Oregon State University |
| | 12 | 361 | Shane Boyd | | P | 21 | 9/18/1982 | | | | | College | | University of Kentucky |
| | 13 | 391 | Walter Patton | | P | 19 | 3/13/1985 | 6-1 | 190 | R | R | Rookie | | Lincoln Land Community College |
| | 14 | 421 | Javi Sanchez | | C | 22 | 11/8/1981 | 6-2 | 200 | R | R | A+ | | University of Notre Dame |
| | 15 | 451 | Juan Portes | | SS | 18 | 11/26/1985 | 5-11 | 170 | R | R | A+ | | Malden High School (Malden,MA) |
| | 16 | 481 | Matt Tolbert | | SS | 22 | 5/4/1982 | 6-0 | 177 | B | R | AAA | | University of Mississippi |
| | 17 | 511 | Eamon Portice | | P | | | | | | | - | | Fort Lauderdale High School (Fort Lauderdale,FL) |
| | 18 | 541 | Josh Rose | | P | | | | | | | - | | Mariner High School (Cape Coral,FL) |
| | 19 | 571 | Tate Casey | | P | | | | | | | - | | Longview High School (Longview,TX) |
| | 20 | 601 | Tim Lahey | | C | 22 | 2/7/1982 | 6-5 | 250 | R | R | AAA | | Princeton University |
| | 21 | 631 | Joseph Abellera | | 3B | 18 | 8/2/1985 | 6-4 | 200 | R | R | Rookie | | Hopkins High School (Minnetonka,MN) |
| | 22 | 661** | Vincent Scarduzio | | P | | | | | | | - | | Jupiter Community High School (Jupiter,FL) |
| | 23 | 691 | Tim Arnold | | P | | | | | | | - | | Fallbrook High School (Fallbrook,CA) |
| | 24 | 721 | Garrett White | | P | 20 | 5/22/1984 | 6-5 | 235 | L | L | A+ | | San Jacinto College-North |
| | 25 | 751 | Joe Welsh | | P | 19 | 9/29/1984 | 6-4 | 180 | L | L | A | | Grand Rapids Community College |
| | 26 | 781 | Deacon Burns | | OF | 21 | 10/28/1982 | 5-8 | 185 | L | L | A+ | | Northern State University |
| | 27 | 811 | Landon Burt | | OF | 21 | 8/16/1982 | 5-10 | 180 | L | L | A | | San Diego State University |
| | 28 | 841 | Aaron Craig | | P | 18 | 3/22/1986 | 6-1 | 205 | R | R | A | | Century High School (Rochester,MN) |
| | 29 | 871 | Ricky Prady | | OF | 19 | 3/5/1985 | 6-3 | 200 | L | R | Ind | | Sebastian River High School (Sebastian,FL) |
| | 30 | 901 | Daniel Berg | | 3B | 19 | 11/21/1984 | 6-0 | 190 | R | R | A | | Texarkana College |
| | 31 | 931 | Jason Laird | | P | | | | | | | - | | Henry County High School (McDonough,GA) |
| | 32 | 961 | Nolan Mulligan | | P | 19 | 1/30/1985 | 6-5 | 190 | R | R | Rookie | | Broward Community College |
| | 33 | 991 | Sean Kalmen | | P | | | | | | | - | | Katella High School (Anaheim,CA) |
| | 34 | 1021** | Rene Tosoni | | OF | 17 | 7/2/1986 | 6-0 | 205 | L | R | A | | Riverside High School (Port Coquitlam,BC) |
| | 35 | 1051 | Jeff Mousser | | P | 22 | 9/10/1981 | 6-2 | 215 | R | R | Rookie | | Arizona State University |
| | 36 | 1081 | John Thies | | P | | | | | | | College | | St. Louis Community College-Meramec |
| | 37 | 1111 | Gregory D'Oleo | | C | | | | | | | - | | Puerto Rico Baseball Academy High School (Gurabo,PR) |
| | 38 | 1141 | Josh Land | | OF | 19 | 2/6/1985 | 6-1 | 185 | L | L | A | | Okaloosa-Walton College |
| | 39 | 1171 | Danny Santiesteban | | OF | 19 | 2/17/1985 | 6-2 | 170 | R | R | A | | Palm Beach Community College |
| | 40 | 1201** | Justin Otto | | P | | | | | | | - | | Chandler High School (Chandler,OK) |
| | 41 | 1231 | Eric Sweeney | | P | | | | | | | - | | Mount Carmel High School (San Diego,CA) |
| | 42 | 1260 | Greg Schilling | | P | 19 | 12/21/1984 | 6-2 | 170 | L | L | - | | Broward Community College |
| | 43 | 1289 | Robbie Hebert | | P | 22 | 12/12/1981 | 6-3 | 210 | R | R | Ind | | Nicholls State University |
| | 44 | 1318 | Tony Joiner | | OF | | | | | | | - | | Haines City High School (Haines City,FL) |
| | 45 | 1347 | Lance Lofton | | 3B | | | | | | | - | | Connally High School (Austin,TX) |
| | 46 | 1376 | Matt Rizzotti | | 1B | 18 | 12/24/1985 | 6-5 | 235 | L | L | A- | | Archbishop Molloy High School (Jamaica,NY) |
| | 47 | 1405 | Chris Petrie | | OF | | | | | | | College | | Lake City Community College |
| | 48 | 1433 | Ryne Nelson | | P | | | | | | | College | | Dickinson High School (Dickinson,TX) |
| | 49 | 1461 | Nicholas Bleau | | P | 18 | 4/14/1986 | 6-1 | 190 | B | L | - | | Gulf Coast Community College |
| | 50 | 1489 | Taylor Cameron | | P | 18 | 7/24/1985 | 6-0 | 210 | R | R | A- | | Cypress College |
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