| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 1 | 1 | 1 | Tidewater | Joba Chamberlain | P |
| 2 | 1 | 2 | Millers Tavern | Dustin McGowan | P |
| 3 | 1 | 3 | Long Island | Ian Kennedy | P |
| 4 | 1 | 4 | East Coast | Kyle Kendrick | P |
| 5 | 1 | 5 | Rhode Island | Hiroki Kuroda (prospect) |
P |
| 6 | 1 | 6 | Louisiana (from Baton Rouge) |
Josh Hamilton | OF |
| 7 | 1 | 7 | Buffalo | Heath Bell | P |
| 8 | 1 | 8 | Gulf Breeze | Mark Reynolds | 3B |
| 9 | 1 | 9 | Green Bay | Shawn Hill | P |
| 10 | 1 | 10 | Texas | Yunel Escobar | SS |
| 11 | 1 | 11 | Greensboro | Peter Moylan | P |
| 12 | 1 | 12 | San Diego | Alexei Ramirez (prospect) |
SS |
| 13 | 1 | 13 | Beantown | Jesse Litsch | P |
| 14 | 1 | 14 | Glab | Brandon Harris | SS |
| 15 | 1 | 15 | Freeport | Matt Wieters (prospect) |
C |
| 16 | 1 | 16 | Millers Tavern (from Chappaqua) |
Steve Pearce | OF |
| 17 | 1 | 17 | Jonesboro | Hideki Okajima | P |
| 18 | 1 | 18 | Baton Rouge (from Mokena) |
J.R. Towles | C |
| 19 | 1 | 19 | Westchester | Lenny Dinardo | P |
| 20 | 1 | 20 | Louisiana (from Tampa) |
Geovany Soto | C |
| 21 | 1 | 21 | Stamford | Franklin Morales | P |
| 22 | 1 | 22 | East Coast (from Arundel) |
Rick Porcello (prospect) |
P |
| 23 | 1 | 23 | Turtle Beach | Asdrubal Cabrera | 2B |
| 24 | 1 | 24 | Chappaqua (from Louisiana) |
Justin Germano | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 25 | 2 | 1 | Tidewater | Jordan Schafer (prospect) |
OF |
| 26 | 2 | 2 | Millers Tavern | Manny Parra | P |
| 27 | 2 | 3 | Long Island | Danny Richar | 2B |
| 28 | 2 | 4 | East Coast | Mike Moustakas (prospect) |
SS |
| 29 | 2 | 5 | Rhode Island | Brandon Morrow | P |
| 30 | 2 | 6 | East Coast (from Baton Rouge) |
Rafael Perez | P |
| 31 | 2 | 7 | Buffalo | Tim Redding | P |
| 32 | 2 | 8 | Gulf Breeze | Carlos Marmol | P |
| 33 | 2 | 9 | Green Bay | Cesar Izturis | SS |
| 34 | 2 | 10 | Texas | Josh Vitters (prospect) |
3B |
| 35 | 2 | 11 | Greensboro | Chas Headley | 3B |
| 36 | 2 | 12 | San Diego | Jeff Keppinger | SS |
| 37 | 2 | 13 | Louisiana (from Beantown) |
Ross Detwiler | P |
| 38 | 2 | 14 | Glab | Ramon Pena | P |
| 39 | 2 | 15 | Freeport | Carlos Carrasco (prospect) |
P |
| 40 | 2 | 16 | Long Island (from Chappaqua) |
Lee Gardner | P |
| 41 | 2 | 17 | Jonesboro | Tony Pena | SS |
| 42 | 2 | 18 | Rhode Island (from Mokena) |
Kosuke Fukodome (prospect) |
OF |
| 43 | 2 | 19 | Westchester | Jack Cust | OF |
| 44 | 2 | 20 | Tampa | Reggie Willits | OF |
| 45 | 2 | 21 | Stamford | Troy Percival | P |
| 46 | 2 | 22 | Arundel | Rick Ankiel | OF |
| 47 | 2 | 23 | Turtle Beach | Austin Jackson (prospect) |
OF |
| 48 | 2 | 24 | Louisiana | Wade Davis (prospect) |
P |
| Overall Pick |
Round number |
Pick number |
Player Selected | Pos | |
| 49 | 3 | 1 | Tidewater | Matt Antonelli (prospect) |
2B |
| 50 | 3 | 2 | Millers Tavern | Wladimir Balentien | OF |
| 51 | 3 | 3 | Long Island | Luis Hernandez | SS |
| 52 | 3 | 4 | East Coast | Brandon Jones | OF |
| 53 | 3 | 5 | Baton Rouge (from Rhode Island) |
Doug Brocail | P |
| 54 | 3 | 6 | Baton Rouge | Rudy Seanez | P |
| 55 | 3 | 7 | Buffalo | Dustin Moseley | P |
| 56 | 3 | 8 | Gulf Breeze | Jair Jurrjens | P |
| 57 | 3 | 9 | Green Bay | Justin Hampson | P |
| 58 | 3 | 10 | Texas | Norris Hopper | OF |
| 59 | 3 | 11 | Greensboro | Jo Jo Reyes | P |
| 60 | 3 | 12 | San Diego | Andy Sonnanstine | P |
| 61 | 3 | 13 | Tidewater (from Beantown) |
Brian Wilson | P |
| 62 | 3 | 14 | Glab | J. C. Romero | P |
| 63 | 3 | 15 | Freeport | Yorman Bazardo | P |
| 64 | 3 | 16 | Chappaqua | Jayson Werth | OF |
| 65 | 3 | 17 | Greensboro (from Jonesboro) |
Ryan Ludwick | OF |
| 66 | 3 | 18 | Mokena | Josh Phelps | C |
| 67 | 3 | 19 | Westchester | Aaron Laffey | P |
| 68 | 3 | 20 | Chappaqua (from Tampa) |
Sergio Mitre | P |
| 69 | 3 | 21 | Stamford | Greg Dobbs | 3B |
| 70 | 3 | 22 | Rhode Island (from Arundel) |
Edinson Volquez | P |
| 71 | 3 | 23 | Turtle Beach | Johnny Cueto (prospect) |
P |
| 72 | 3 | 24 | Louisiana | Bobby Seay | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 73 | 4 | 1 | Tidewater | Matt Chico | P |
| 74 | 4 | 2 | Millers Tavern | Jonathan Meloan | P |
| 75 | 4 | 3 | Long Island | Christian Guzman | SS |
| 76 | 4 | 4 | East Coast | Joe Thatcher | P |
| 77 | 4 | 5 | Rhode Island | Nick Blackburn | P |
| 78 | 4 | 6 | Baton Rouge | Joe Borowski | P |
| 79 | 4 | 7 | Buffalo | Chad Durbin | P |
| 80 | 4 | 8 | Gulf Breeze | Felipe Paulino | P |
| 81 | 4 | 9 | Green Bay | Nelson Cruz | OF |
| 82 | 4 | 10 | Texas | Willie Harris | OF |
| 83 | 4 | 11 | East Coast (from Greensboro) |
Aaron Boone | 1B |
| 84 | 4 | 12 | San Diego | Kevin Cameron | P |
| 85 | 4 | 13 | Beantown | Leo Nunez | P |
| 86 | 4 | 14 | Glab | Justin Miller | P |
| 87 | 4 | 15 | Freeport | Jared Burton | P |
| 88 | 4 | 16 | Chappaqua | Matt Herges | P |
| 89 | 4 | 17 | Jonesboro | Buddy Carlyle | P |
| 90 | 4 | 18 | Mokena | Jerry Owens | OF |
| 91 | 4 | 19 | Westchester | Jesus Flores | C |
| 92 | 4 | 20 | Tampa | Nate Schierholtz | OF |
| 93 | 4 | 21 | Stamford | Brian Wolfe | P |
| 94 | 4 | 22 | Chappaqua (from Arundel) |
Rob Bowen | C |
| 95 | 4 | 23 | Turtle Beach | Santiago Casilla | P |
| 96 | 4 | 24 | Louisiana | Chris Schroder | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 97 | 5 | 1 | Tidewater | Al Reyes | P |
| 98 | 5 | 2 | Beantown (from Millers Tavern) |
Ruben Gotay | 2B |
| 99 | 5 | 3 | Long Island | Dave Dellucci | OF |
| 100 | 5 | 4 | East Coast | Mike Rabelo | C |
| 101 | 5 | 5 | Rhode Island | Kyle Farnsworth | P |
| 102 | 5 | 6 | Baton Rouge | Sean Green | P |
| 103 | 5 | 7 | Buffalo | Mike Timlin | P |
| 104 | 5 | 8 | Gulf Breeze | Jennsen Lewis | P |
| 105 | 5 | 9 | Green Bay | Eric O'Flaherty | P |
| 106 | 5 | 10 | Texas | Ryan Klesko | 1B |
| 107 | 5 | 11 | Greensboro | Matt LaPorta (prospect) |
1B |
| 108 | 5 | 12 | San Diego | Mike Fontenot | 2B |
| 109 | 5 | 13 | Millers Tavern (from Beantown) |
Luis Ayala | P |
| 110 | 5 | 14 | Glab | Rajai Davis | OF |
| 111 | 5 | 15 | Freeport | Jesus Colome | P |
| 112 | 5 | 16 | Freeport (from Chappaqua) |
David Murphy | OF |
| 113 | 5 | 17 | Jonesboro | Scott Spiezio | 3B |
| 114 | 5 | 18 | Mokena | Tony Abreu | 3B |
| 115 | 5 | 19 | Westchester | Ryan Rowland Smith | P |
| 116 | 5 | 20 | Tampa | Mike Lieberthal | C |
| 117 | 5 | 21 | Stamford | Javier Lopez | P |
| 118 | 5 | 22 | Arundel | Chin-Lung Hu | SS |
| 119 | 5 | 23 | Turtle Beach | Radhames Liz | P |
| 120 | 5 | 24 | Louisiana | Chris Marrero (prospect) |
1B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 121 | 6 | 1 | Tidewater | Brendan Ryan | SS |
| 122 | 6 | 2 | Millers Tavern | James Hoey | P |
| 123 | 6 | 3 | Long Island | Ryan Raburn | OF |
| 124 | 6 | 4 | East Coast | Edwin Jackson | P |
| 125 | 6 | 5 | Rhode Island | Tyler Clippard | P |
| 126 | 6 | 6 | Baton Rouge | Ramon Vazquez | 3B |
| 127 | 6 | 7 | Buffalo | Masahide Kobayashi (prospect) |
P |
| 128 | 6 | 8 | Gulf Breeze | Daniel Cortes (prospect) |
P |
| 129 | 6 | 9 | Green Bay | Jason Larue | C |
| 130 | 6 | 10 | Texas | Kip Wells | P |
| 131 | 6 | 11 | Greensboro | Desmond Jennings | OF |
| 132 | 6 | 12 | San Diego | Jamie Burke | C |
| 133 | 6 | 13 | Beantown | Skip Schumaker | OF |
| 134 | 6 | 14 | Glab | Chris Bootcheck | P |
| 135 | 6 | 15 | Chappaqua (from Freeport through Rhode Island) |
Shelley Duncan | OF |
| 136 | 6 | 16 | Millers Tavern (from Chappaqua) |
Jarrod Parker (prospect) |
P |
| 137 | 6 | 17 | Jonesboro | Trot Nixon | OF |
| 138 | 6 | 18 | Mokena | Lance Broadway | P |
| 139 | 6 | 19 | Westchester | Tony Clark | 1B |
| 140 | 6 | 20 | Tampa | Jeff Niemann (prospect) |
P |
| 141 | 6 | 21 | Stamford | Taylor Teagarden (prospect) |
C |
| 142 | 6 | 22 | Chappaqua (from Arundel) |
Garrett Olson | P |
| 143 | 6 | 23 | Turtle Beach | Joe Smith | P |
| 144 | 6 | 24 | Chappaqua (from Louisiana) |
Delwyn Young | OF |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 145 | 7 | 1 | Tidewater | Rick Vanden Hurk | P |
| 146 | 7 | 2 | Millers Tavern | Brandon Moss |
OF |
| 147 | 7 | 3 | Long Island | Augie Ojeda | 2B |
| 148 | 7 | 4 | East Coast | Clint Barmes | SS |
| 149 | 7 | 5 | Rhode Island | Randy Flores | P |
| 150 | 7 | 6 | Baton Rouge | Jason Phillips | C |
| 151 | 7 | 7 | Buffalo | Gary Glover | P |
| 152 | 7 | 8 | Gulf Breeze | Jayson Nix (prospect) |
2B |
| 153 | 7 | 9 | Green Bay | Randy Messenger | P |
| 154 | 7 | 10 | Texas | Brian Moehler | P |
| 155 | 7 | 11 | San Diego (from Greensboro) |
Brian Barton (prospect) |
OF |
| 156 | 7 | 12 | San Diego | Chris Heintz | C |
| 157 | 7 | 13 | Beantown | Dan Ortmeier | OF |
| 158 | 7 | 14 | Glab | Chris Perez (prospect) |
P |
| 159 | 7 | 15 | Freeport | Frank Francisco | P |
| 160 | 7 | 16 | Chappaqua | Nyjer Morgan | OF |
| 161 | 7 | 17 | Jonesboro | Josh Anderson | OF |
| 162 | 7 | 18 | San Diego (fom Mokena) |
Seth Smith | OF |
| 163 | 7 | 19 | Westchester | Jack Egbert (prospect) |
P |
| 164 | 7 | 20 | Tampa | Trever Miller | P |
| 165 | 7 | 21 | Stamford | Jack Hannahan | 3B |
| 166 | 7 | 22 | Arundel | Justin Maxwell | OF |
| 167 | 7 | 23 | Turtle Beach | Doug Slaten | P |
| 168 | 7 | 24 | Louisiana | Alan Horne (prospect) |
P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 169 | 8 | 1 | Tidewater | Jonathan Albaladejo | P |
| 170 | 8 | 2 | Stamford (from Millers Tavern) |
Chris Volstad (prospect) |
P |
| 171 | 8 | 3 | Long Island | Eric Munson | C |
| 172 | 8 | 4 | Westchester (from East Coast) |
Wade Leblanc (prospect) |
P |
| 173 | 8 | 5 | Rhode Island | Billy Buckner | P |
| 174 | 8 | 6 | Baton Rouge | Mike Bacsik | P |
| 175 | 8 | 7 | Buffalo | Steve Trachsel | P |
| 176 | 8 | 8 | Gulf Breeze | Chin-Hui Tsao | P |
| 177 | 8 | 9 | Green Bay | Koyie Hill | C |
| 178 | 8 | 10 | Texas | Tim Byrdak | P |
| 179 | 8 | 11 | Jonesboro (from Greensboro) |
Clint Sammons | C |
| 180 | 8 | 12 | Mokena (from San Diego) |
Jose Ascanio | P |
| 181 | 8 | 13 | Beantown | Jeff Bennett | P |
| 182 | 8 | 14 | Glab | Bryan Anderson (prospect) |
C |
| 183 | 8 | 15 | Freeport | Waiver loss | |
| 184 | 8 | 16 | Chappaqua | Chris Lubanski (prospect) |
OF |
| 185 | 8 | 17 | Jonesboro | Micah Bowie | P |
| 186 | 8 | 18 | Mokena | Raul Casanova | C |
| 187 | 8 | 19 | Westchester | Donnie Murphy | SS |
| 188 | 8 | 20 | Tampa | Ryan Sweeney | OF |
| 189 | 8 | 21 | Stamford | Guillermo Rodriguez | C |
| 190 | 8 | 22 | Arundel | Manny Acosta | P |
| 191 | 8 | 23 | Turtle Beach | Brayan Pena | C |
| 192 | 8 | 24 | Louisiana | Luis Mendoza |
P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 193 | 9 | 1 | Beantown (from Tidewater) |
Pat Misch | P |
| 194 | 9 | 2 | Louisiana (from Millers Tavern) |
Ehren Wassermann | P |
| 195 | 9 | 3 | Long Island | Josh Wilson | SS |
| 196 | 9 | 4 | East Coast | Adam Eaton | P |
| 197 | 9 | 5 | Rhode Island | Jarod Plummer (prospect) |
P |
| 198 | 9 | 6 | Baton Rouge | Jeff Weaver | P |
| 199 | 9 | 7 | Buffalo | Aaron Poreda (prospect) |
P |
| 200 | 9 | 8 | Gulf Breeze | Andrew Brown | P |
| 201 | 9 | 9 | Green Bay | Jaime Garcia (prospect) |
P |
| 202 | 9 | 10 | Texas | Carlos Triunfel (prospect) |
SS |
| 203 | 9 | 11 | Greensboro | Max Scherzer (prospect) |
P |
| 204 | 9 | 12 | Mokena (from San Diego) |
Jose Ceda (prospect) |
P |
| 205 | 9 | 13 | Beantown | Bobbie Brownlie (prospect) |
P |
| 206 | 9 | 14 | Glab | Eugenio Velez | 2B |
| 207 | 9 | 15 | Freeport | Cha-Seung Baek | P |
| 208 | 9 | 16 | Louisiana (from Chappaqua) |
Dallas Braden | P |
| 209 | 9 | 17 | Jonesboro | Gregor Blanco (prospect) |
OF |
| 210 | 9 | 18 | Mokena | Travis Metcalf | 3B |
| 211 | 9 | 19 | Westchester | Kevin Hart | P |
| 212 | 9 | 20 | Tampa | Nick Weglarz (prospect) |
OF |
| 213 | 9 | 21 | Stamford | Henry Owens | P |
| 214 | 9 | 22 | Arundel | Timo Perez | OF |
| 215 | 9 | 23 | Turtle Beach | Donny Lucy | C |
| 216 | 9 | 24 | Louisiana | Eric Patterson | OF |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 217 | 10 | 1 | Tidewater | Edwar Ramirez | P |
| 218 | 10 | 2 | Chappaqua (from Millers Tavern) |
Kevin Mulvey (prospect) |
P |
| 219 | 10 | 3 | Long Island | Elvis Andrus (prospect) |
SS |
| 220 | 10 | 4 | East Coast | Odalis Perez | P |
| 221 | 10 | 5 | Rhode Island | Pass | |
| 222 | 10 | 6 | Baton Rouge | Pass | |
| 223 | 10 | 7 | Buffalo | Darin Erstad | OF |
| 224 | 10 | 8 | Gulf Breeze | Josh Paul | C |
| 225 | 10 | 9 | Green Bay | Angel Villalona (prospect) |
3B |
| 226 | 10 | 10 | Freeport (from Texas through Chappaqua, Millers Tavern, and Chappaqua) |
Andrew Carignan (prospect) |
P |
| 227 | 10 | 11 | Greensboro | Jason Heyward (prospect) |
OF |
| 228 | 10 | 12 | Mokena (from San Diego) | Michael Bowden (prospect) |
P |
| 229 | 10 | 13 | Beantown | Oswaldo Navarro (prospect) |
SS |
| 230 | 10 | 14 | Glab | Brian Duensing (prospect) |
P |
| 231 | 10 | 15 | Freeport | Robby Hammock | c |
| 232 | 10 | 16 | Arundel (from Chappaqua) |
John Lannan | P |
| 233 | 10 | 17 | Jonesboro | Tyler Yates | P |
| 234 | 10 | 18 | Stamford (from Mokena) |
Eric Bruntlett | SS |
| 235 | 10 | 19 | Westchester | Juan Gutierrez | P |
| 236 | 10 | 20 | Freeport (from Tampa) |
Tom Mastny | P |
| 237 | 10 | 21 | Stamford | Emilio Bonifacio | 2B |
| 238 | 10 | 22 | Arundel | Brandon League | P |
| 239 | 10 | 23 | Turtle Beach | Jorge de la Rosa | P |
| 240 | 10 | 24 | Louisiana | Tyler Walker | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 241 | 11 | 1 | Tidewater | Sam Fuld | OF |
| 242 | 11 | 2 | Chappaqua (from Millers Tavern) |
Robert Andino | SS |
| 243 | 11 | 3 | Long Island | J.D. Durbin | P |
| 244 | 11 | 4 | East Coast | Pass | |
| 245 | 11 | 5 | Arundel (from Rhode Island) |
Eulogio de la Cruz | P |
| 246 | 11 | 6 | Baton Rouge | Pass | |
| 247 | 11 | 7 | Buffalo | Kameron Loe | P |
| 248 | 11 | 8 | Gulf Breeze | Alex Cora | 2B |
| 249 | 11 | 9 | Green Bay | Matt Latos (prospect) |
P |
| 250 | 11 | 10 | Texas | Mark Kotsay | OF |
| 251 | 11 | 11 | Greensboro | Royce Ring | P |
| 252 | 11 | 12 | San Diego | Pass | |
| 253 | 11 | 13 | Chappaqua (from Beantown through Millers Tavern) |
Matt Wise | P |
| 254 | 11 | 14 | Glab | Mike Sweeney | 1B |
| 255 | 11 | 15 | Arundel (from Freeport through Chappaqua) |
JJ Furmaniak | SS |
| 256 | 11 | 16 | Arundel (from Chappaqua) |
Pedro Alvarez (prospect) |
3B |
| 257 | 11 | 17 | Jonesboro | Pass | |
| 258 | 11 | 18 | Mokena | Daniel Moskos (prospect) |
P |
| 259 | 11 | 19 | Westchester | Pass | |
| 260 | 11 | 20 | Tampa | John Jaso (prospect) |
C |
| 261 | 11 | 21 | Stamford | Ben Francisco | OF |
| 262 | 11 | 22 | Arundel | Fautino De Los Santos (prospect) |
P |
| 263 | 11 | 23 | Turtle Beach | Korey Casto | OF |
| 264 | 11 | 24 | Louisiana | D'Angelo Jimenez |
2B |
|
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| XTR | 1 | ||||
| XTR | 2 |