| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 1 | 1 | 1 | Mokena | Everth Cabrera | SS |
| 2 | 1 | 2 | Buffalo | Randy Wells | P |
| 3 | 1 | 3 | Beantown | Brad Bergesen | P |
| 4 | 1 | 4 | Pike City | Ricky Romero | P |
| 5 | 1 | 5 | Chappaqua | Andrew Bailey | P |
| 6 | 1 | 6 | East Coast | Desmond Jennings (prospect) |
OF |
| 7 | 1 | 7 | San Diego | Ronald Belisario | P |
| 8 | 1 | 8 | Freeport | Aroldis Chapman (prospect) |
P |
| 9 | 1 | 9 | Long Island | Casey McGehee | 3B |
| 10 | 1 | 10 | Millers Tavern | Scott Sizemore (prospect) |
2B |
| 11 | 1 | 11 | Arundel | Chris Coghlan | OF |
| 12 | 1 | 12 | Greensboro | Kyle Blanks | OF |
| 13 | 1 | 13 | Jonesboro | Tommy Hunter | P |
| 14 | 1 | 14 | Green Bay | Jonny Gomes | OF |
| 15 | 1 | 15 | Turtle Beach | Garrett Jones | OF |
| 16 | 1 | 16 | Arundel (from Baton Rouge) | Ian Desmond | SS |
| 17 | 1 | 17 | Tampa | Marc Rzepcyznski | P |
| 18 | 1 | 18 | Gulf Breeze | Darren O'Day | P |
| 19 | 1 | 19 | Glab | David Aardsma | P |
| 20 | 1 | 20 | Stamford | Gerardo Parra |
OF |
| 21 | 1 | 21 | Staten Island | Dan Hudson | P |
| 22 | 1 | 22 | Pike City (from Westchester) | Kyle Drabek (prospect) |
P |
| 23 | 1 | 23 | Louisiana | Dustin Ackley (prospect) |
2B |
| 24 | 1 | 24 | Tidewater | Freddie Freeman (prospect) |
1B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 25 | 2 | 1 | Mokena | Omir Santos | C |
| 26 | 2 | 2 | Buffalo | Luke Gregerson | P |
| 27 | 2 | 3 | Beantown | Matt Palmer | P |
| 28 | 2 | 4 | Pike City | Bud Norris | P |
| 29 | 2 | 5 | Chappaqua | Ryan Roberts | 2B |
| 30 | 2 | 6 | East Coast | Alex Avila | C |
| 31 | 2 | 7 | San Diego | Jason Jaramillo | C |
| 32 | 2 | 8 | Freeport | Domonic Brown (prospect) |
OF |
| 33 | 2 | 9 | Long Island | JD Martin | P |
| 34 | 2 | 10 | Millers Tavern | Daniel Bard | P |
| 35 | 2 | 11 | Arundel | Drew Stubbs | OF |
| 36 | 2 | 12 | Arundel (from Greensboro) | Sean West | P |
| 37 | 2 | 13 | Jonesboro | Charlie Morton | P |
| 38 | 2 | 14 | Green Bay | Martin Perez (prospect) |
P |
| 39 | 2 | 15 | Turtle Beach | CJ Wilson | P |
| 40 | 2 | 16 | East Coast (from Baton Rouge) | Vin Mazzaro | P |
| 41 | 2 | 17 | Tampa | Todd Coffey | P |
| 42 | 2 | 18 | Gulf Breeze | Emilio Bonifacio | 3B |
| 43 | 2 | 19 | Glab | Kiko Calero | P |
| 44 | 2 | 20 | Stamford | Rafeal Betancourt | P |
| 45 | 2 | 21 | Staten Island | Josh Thole | C |
| 46 | 2 | 22 | Westchester | Sean Burnett | P |
| 47 | 2 | 23 | Louisiana | Jordan Zimmermann | P |
| 48 | 2 | 24 | Tidewater | Brian Sanches | P |
| Overall Pick |
Round number |
Pick number |
Player Selected | Pos | |
| 49 | 3 | 1 | Mokena | Ronny Cedeno | SS |
| 50 | 3 | 2 | Buffalo | Tony Gwynn | OF |
| 51 | 3 | 3 | Beantown | Geoff Blum | 3B |
| 52 | 3 | 4 | Greensboro (from Pike City) | Casey Kelly (prospect) |
P |
| 53 | 3 | 5 | Chappaqua | Craig Stammen | P |
| 54 | 3 | 6 | East Coast | Brandon Allen | 1B |
| 55 | 3 | 7 | San Diego | Juan Francisco | 3B |
| 56 | 3 | 8 | Freeport | Kris Medlen | P |
| 57 | 3 | 9 | Long Island | Hernan Iribarren | 2B |
| 58 | 3 | 10 | Millers Tavern | Eric Young | 2B |
| 59 | 3 | 11 | Arundel | Adam Moore | C |
| 60 | 3 | 12 | Greensboro | Chris C. Carter (prospect) |
1B |
| 61 | 3 | 13 | Jonesboro | Brian Tallet | P |
| 62 | 3 | 14 | Green Bay | Jayson Nix | 2B |
| 63 | 3 | 15 | Turtle Beach | Joe Thatcher | P |
| 64 | 3 | 16 | Baton Rouge | Blake Hawksworth | P |
| 65 | 3 | 17 | Tampa | Michael Brantley | OF |
| 66 | 3 | 18 | Buffalo (from Gulf Breeze) | Donovan Tate (prospect) |
OF |
| 67 | 3 | 19 | Glab | Sean White | P |
| 68 | 3 | 20 | Stamford | Drew Storen (prospect) |
P |
| 69 | 3 | 21 | Staten Island | Michael Taylor (prospect) |
OF |
| 70 | 3 | 22 | Westchester | Tim Stauffer | P |
| 71 | 3 | 23 | Louisiana | David Robertson | P |
| 72 | 3 | 24 | Tidewater | Tyler Clippard | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 73 | 4 | 1 | Mokena | Starlin Castro (prospect) |
SS |
| 74 | 4 | 2 | Buffalo | Scott Richmond | P |
| 75 | 4 | 3 | Beantown | Jake Fox | 3B |
| 76 | 4 | 4 | Pike City | Josh Fields | 3B |
| 77 | 4 | 5 | Long Island (from Chappaqua) | Clete Thomas | OF |
| 78 | 4 | 6 | East Coast | Devaris (Dee) Gordon (prospect) |
SS |
| 79 | 4 | 7 | San Diego | Robinzon Diaz | C |
| 80 | 4 | 8 | Freeport | Troy Glaus | 3B |
| 81 | 4 | 9 | Long Island | Daniel McCutchen | P |
| 82 | 4 | 10 | Millers Tavern | Dan Schlereth | P |
| 83 | 4 | 11 | Arundel | Michael Saunders | OF |
| 84 | 4 | 12 | Greensboro | Eric O'Flaherty | P |
| 85 | 4 | 13 | Jonesboro | Brandon Medders | P |
| 86 | 4 | 14 | Green Bay | Fred Lewis | OF |
| 87 | 4 | 15 | Turtle Beach | Claudio Vargas | P |
| 88 | 4 | 16 | Baton Rouge | Rich Hill | P |
| 89 | 4 | 17 | Tampa | Daniel Ray Herrera | P |
| 90 | 4 | 18 | Gulf Breeze | Felipe Paulino | P |
| 91 | 4 | 19 | Glab | Koyie Hill | C |
| 92 | 4 | 20 | Stamford | Angel Guzman | P |
| 93 | 4 | 21 | Staten Island | Mitchell Boggs | P |
| 94 | 4 | 22 | Westchester | Brad Lincoln (prospect) |
P |
| 95 | 4 | 23 | Louisiana | Mike Montgomery (prospect) |
P |
| 96 | 4 | 24 | Tidewater | Christian Friedrich (prospect) |
P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 97 | 5 | 1 | Mokena | Josh Bell (prospect) |
3B |
| 98 | 5 | 2 | Turtle Beach (from Buffalo) | Jaff Decker (prospect) |
OF |
| 99 | 5 | 3 | Beantown | Andres Torres | OF |
| 100 | 5 | 4 | Pike City | Neil Walker | 3B |
| 101 | 5 | 5 | Freeport (from Chappaqua) | Shairon Martis | OF |
| 102 | 5 | 6 | East Coast | Shelby Miller (prospect) |
P |
| 103 | 5 | 7 | San Diego | Jose Iglesias (prospect) |
SS |
| 104 | 5 | 8 | Freeport | Fernando Nieve | P |
| 105 | 5 | 9 | Turtle Beach (from Long Island) | Josh Reddick | OF |
| 106 | 5 | 10 | Millers Tavern | Rick Vandenhurk | P |
| 107 | 5 | 11 | Arundel | Alex Gonzalez | SS |
| 108 | 5 | 12 | Greensboro | Shaun Marcum | P |
| 109 | 5 | 13 | Jonesboro | Jeff Fulchino | P |
| 110 | 5 | 14 | Green Bay | Dan Meyers | P |
| 111 | 5 | 15 | Turtle Beach | DJ Carrasco | P |
| 112 | 5 | 16 | Baton Rouge | Edward Mujica | P |
| 113 | 5 | 17 | Tampa | Aaron Hicks (prospect) |
OF |
| 114 | 5 | 18 | San Diego (from Buffalo through Gulf Breeze) | Jose Morales | C |
| 115 | 5 | 19 | Chappaqua (from Glab) | Jose Tabata (prospect) |
OF |
| 116 | 5 | 20 | Arundel (from Stamford) | Jason Bulger | P |
| 117 | 5 | 21 | Staten Island | David Hernandez | P |
| 118 | 5 | 22 | Westchester | Clay Zavada | P |
| 119 | 5 | 23 | Louisiana | Ryan Westmoreland (prospect) |
OF |
| 120 | 5 | 24 | Tidewater | Mike Aviles | SS |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 121 | 6 | 1 | Mokena | Jeff Francis | P |
| 122 | 6 | 2 | Buffalo | Jason Vargas | P |
| 123 | 6 | 3 | Beantown | Burke Badenhop | P |
| 124 | 6 | 4 | Pike City | Glen Perkins | P |
| 125 | 6 | 5 | San Diego (from Chappaqua) | Oscar Salazar | OF |
| 126 | 6 | 6 | East Coast | Dan Runzler | P |
| 127 | 6 | 7 | San Diego | Luis Durango | OF |
| 128 | 6 | 8 | Freeport | Evan Meek | P |
| 129 | 6 | 9 | Stamford (from Long Island) | Raul Chavez | C |
| 130 | 6 | 10 | Millers Tavern | Sergio Romo | P |
| 131 | 6 | 11 | Arundel | Rob Johnson | C |
| 132 | 6 | 12 | Greensboro | Alberto Arias | P |
| 133 | 6 | 13 | Jonesboro | Bob Howry | P |
| 134 | 6 | 14 | Green Bay | Chad Tracy | 1B |
| 135 | 6 | 15 | Turtle Beach | Randy Ruiz | 1B |
| 136 | 6 | 16 | Baton Rouge | Jeff Weaver | P |
| 137 | 6 | 17 | Tampa | Landon Powell | C |
| 138 | 6 | 18 | Glab (from Gulf Breeze) | Mitch Maier | OF |
| 139 | 6 | 19 | Glab | Ramiro Pena | SS |
| 140 | 6 | 20 | Stamford | Brendan Donnelly | P |
| 141 | 6 | 21 | Staten Island | Adam Rosales | 3B |
| 142 | 6 | 22 | Westchester | Chris Withrow (prospect) |
P |
| 143 | 6 | 23 | Louisiana | Lance Nix | OF |
| 144 | 6 | 24 | Tidewater | Luke French | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 145 | 7 | 1 | Mokena | Doug Fister | P |
| 146 | 7 | 2 | Turtle Beach (from Buffalo) | Sammy Gervacio | P |
| 147 | 7 | 3 | Beantown | Micah Hoffpauir | OF |
| 148 | 7 | 4 | Pike City | Pass (UWC) | |
| 149 | 7 | 5 | Chappaqua | Todd Frazier (prospect) |
3B |
| 150 | 7 | 6 | East Coast | Guillermo Mota | P |
| 151 | 7 | 7 | San Diego | Jamie Hoffman | OF |
| 152 | 7 | 8 | Freeport | Alex Cora | SS |
| 153 | 7 | 9 | Long Island | Billy Buckner | P |
| 154 | 7 | 10 | Millers Tavern | Matt Moore (prospect) |
P |
| 155 | 7 | 11 | Arundel | Tony Sipp | P |
| 156 | 7 | 12 | Greensboro | Trevor Crowe | OF |
| 157 | 7 | 13 | Jonesboro | Nick Green | SS |
| 158 | 7 | 14 | Green Bay | Mark Difelice | P |
| 159 | 7 | 15 | Buffalo (from Turtle Beach) | Ton Sanchez (prospect) |
C |
| 160 | 7 | 16 | Baton Rouge | Juan Gutierrez | P |
| 161 | 7 | 17 | Tampa | Steven Jackson | P |
| 162 | 7 | 18 | Gulf Breeze | Danys Baez | P |
| 163 | 7 | 19 | Gulf Breeze (from Glab) | Mitch Stetter | P |
| 164 | 7 | 20 | Stamford | Michael Aubrey | 1B |
| 165 | 7 | 21 | Staten Island | Kevin Hart | P |
| 166 | 7 | 22 | Westchester | Tyler Greene | SS |
| 167 | 7 | 23 | Louisiana | Justin Maxwell | OF |
| 168 | 7 | 24 | Tidewater | Matt Tolbert | 2B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 169 | 8 | 1 | Mokena | Alexi Casilla | 2B |
| 170 | 8 | 2 | Gulf Breeze (from Buffalo) | Randy Choate | P |
| 171 | 8 | 3 | Beantown | Nelson Figueroa | P |
| 172 | 8 | 4 | Pike City | Pass (UWC) | |
| 173 | 8 | 5 | Chappaqua | Brian Stokes | P |
| 174 | 8 | 6 | East Coast | Omar Vizquel | SS |
| 175 | 8 | 7 | San Diego | Trent Oeltjen | OF |
| 176 | 8 | 8 | Freeport | Blaine Boyer | P |
| 177 | 8 | 9 | Long Island | Trevor Bell | P |
| 178 | 8 | 10 | Millers Tavern | Wilkin Ramirez | OF |
| 179 | 8 | 11 | Arundel | Casey Crosby (prospect) |
P |
| 180 | 8 | 12 | Greensboro | Tommy Manzella | SS |
| 181 | 8 | 13 | Jonesboro | Mike Sweeney | 1B |
| 182 | 8 | 14 | Green Bay | Derek Norris (prospect) |
C |
| 183 | 8 | 15 | Turtle Beach | Sam Fuld | OF |
| 184 | 8 | 16 | Baton Rouge | Mark Hendrickson | P |
| 185 | 8 | 17 | Tampa | Matt Dominguez (prospect) |
3B |
| 186 | 8 | 18 | Gulf Breeze | Eric Patterson | OF |
| 187 | 8 | 19 | Glab | Jordan Walden (prospect) |
P |
| 188 | 8 | 20 | Stamford | Jenrry Mejia (prospect) |
P |
| 189 | 8 | 21 | Staten Island | Chris Pettit | OF |
| 190 | 8 | 22 | Westchester | John Mayberry, Jr. | OF |
| 191 | 8 | 23 | Louisiana | Andres Blanco | 2B |
| 192 | 8 | 24 | Tidewater | Jason Motte | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 193 | 9 | 1 | Mokena | Terry Evans | OF |
| 194 | 9 | 2 | Buffalo | Mike Minor (prospect) |
P |
| 195 | 9 | 3 | Beantown | Doug Mathis | P |
| 196 | 9 | 4 | Pike City | Zach Britton (prospect) |
P |
| 197 | 9 | 5 | Baton Rouge (from Chappaqua) | Charlie Haeger | P |
| 198 | 9 | 6 | East Coast | Robert Andino | SS |
| 199 | 9 | 7 | San Diego | Hank Conger (prospect) |
C |
| 200 | 9 | 8 | Freeport | Miguel Batista | P |
| 201 | 9 | 9 | Chappaqua (from Long Island) | Carlos Villanueva | P |
| 202 | 9 | 10 | Millers Tavern | Junichi Tazawa | P |
| 203 | 9 | 11 | Arundel | Esmailan Caridad | P |
| 204 | 9 | 12 | Greensboro | Sean O'Sullivan | P |
| 205 | 9 | 13 | Jonesboro | Jason Jennings | P |
| 206 | 9 | 14 | Green Bay | Eli Whiteside | C |
| 207 | 9 | 15 | Turtle Beach | Isaac Davis (prospect) |
1B |
| 208 | 9 | 16 | Baton Rouge | Brad Thompson | P |
| 209 | 9 | 17 | Tampa | Angel Salome (prospect) |
C |
| 210 | 9 | 18 | Gulf Breeze | Jeff Clement | C |
| 211 | 9 | 19 | Glab | Hisanori Takahaski (prospect) |
P |
| 212 | 9 | 20 | Stamford | Tyler Walker | P |
| 213 | 9 | 21 | Staten Island | Jeff Larish | 1B |
| 214 | 9 | 22 | Westchester | David Weathers | P |
| 215 | 9 | 23 | Louisiana | Brad Kilby | P |
| 216 | 9 | 24 | Tidewater | Matt Maloney | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 217 | 10 | 1 | Mokena | Mike MacDougal | P |
| 218 | 10 | 2 | Buffalo | Joe Thurston | 3B |
| 219 | 10 | 3 | Beantown | Kevin Millar | 1B |
| 220 | 10 | 4 | Pike City | Eliezer Alfonzo | C |
| 221 | 10 | 5 | Chappaqua | Paul Janish | SS |
| 222 | 10 | 6 | East Coast | Jamie Burke | C |
| 223 | 10 | 7 | San Diego | Pass | |
| 224 | 10 | 8 | Freeport | Bobby Scales | OF |
| 225 | 10 | 9 | Long Island | Mike Carp | 1B |
| 226 | 10 | 10 | Millers Tavern | Eric Chavez | 3B |
| 227 | 10 | 11 | Arundel | Matt Harrison | P |
| 228 | 10 | 12 | Greensboro | Mark Melancon | P |
| 229 | 10 | 13 | Jonesboro | Sean Green | P |
| 230 | 10 | 14 | Green Bay | Brett Lawrie (prospect) |
2B |
| 231 | 10 | 15 | Turtle Beach | Drew Sutton | 2B |
| 232 | 10 | 16 | Baton Rouge | Kevin Gregg | P |
| 233 | 10 | 17 | Tampa | Josh Wilson | SS |
| 234 | 10 | 18 | Gulf Breeze | Zach Stewart (prospect) |
P |
| 235 | 10 | 19 | Glab | Jeff Gray | P |
| 236 | 10 | 20 | Stamford | Antonio Bastardo | P |
| 237 | 10 | 21 | Staten Island | Chris Narveson | P |
| 238 | 10 | 22 | Westchester | Brett Carroll | OF |
| 239 | 10 | 23 | Louisiana | Kevin Jepsen | P |
| 240 | 10 | 24 | Tidewater | Tobi Stoner | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 241 | 11 | 1 | Mokena | Kyle Farnsworth | P |
| 242 | 11 | 2 | Buffalo | Mike Redmond | C |
| 243 | 11 | 3 | Beantown | Ethan Martin (prospect) |
P |
| 244 | 11 | 4 | Pike City | Jess Chavez | P |
| 245 | 11 | 5 | Stamford (from Chappaqua) | Endy Chavez | OF |
| 246 | 11 | 6 | East Coast | Steve Pearce | 1B |
| 247 | 11 | 7 | Chappaqua (from San Diego) |
Trevor Reckling (prospect) |
P |
| 248 | 11 | 8 | Freeport | Michel Hernandez | C |
| 249 | 11 | 9 | Long Island | Andy Marte | 1B |
| 250 | 11 | 10 | Millers Tavern | Ryan Freel | OF |
| 251 | 11 | 11 | Arundel | Lonnie Chisenhall (prospect) |
3B |
| 252 | 11 | 12 | Greensboro | Bobby Wilson | C |
| 253 | 11 | 13 | Jonesboro | Russ Springer | P |
| 254 | 11 | 14 | Green Bay | Pass | |
| 255 | 11 | 15 | Turtle Beach | Brad Ausmus | C |
| 256 | 11 | 16 | Chappaqua (from Baton Rouge) | Jay Jackson (prospect) |
P |
| 257 | 11 | 17 | Tampa | Kelvim Escobar | P |
| 258 | 11 | 18 | Gulf Breeze | Jared Mitchell (prospect) |
OF |
| 259 | 11 | 19 | Glab | Dewayne Wise | OF |
| 260 | 11 | 20 | Stamford | Brett Tomko | P |
| 261 | 11 | 21 | Staten Island | Jeremy Accardo | P |
| 262 | 11 | 22 | Westchester | Mike Morse | 1B |
| 263 | 11 | 23 | Louisiana | Chris Gimenez | OF |
| 264 | 11 | 24 | Tidewater | Brent Lillibridge | 2B |
|
|
|
|
|
|
| XTR | 1 | Pike City | Alfredo Amezaga | OF | |
| XTR | 2 | Pike City | Mark Loretta | 3B | |
| XTR | 3 | ||||
| XTR | 4 |