| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 1 | 1 | 1 | Beantown | Amando Galarraga | P |
| 2 | 1 | 2 | Pike City | Blake DeWitt | 2B |
| 3 | 1 | 3 | Buffalo | Michael Bourn | OF |
| 4 | 1 | 4 | Millers Tavern | Chris Davis | 1B |
| 5 | 1 | 5 | Staten Island | Jose Arredondo | P |
| 6 | 1 | 6 | Tampa | Dana Eveland | P |
| 7 | 1 | 7 | Arundel | Mike Aviles | SS |
| 8 | 1 | 8 | Long Island | Shin-Soo Choo | OF |
| 9 | 1 | 9 | Turtle Beach | Hong-Chih Kuo | P |
| 10 | 1 | 10 | Greensboro | Pablo Sandoval | 1B |
| 11 | 1 | 11 | Baton Rouge | Clint Barmes | 2B |
| 12 | 1 | 12 | Chappaqua | Greg Smith | P |
| 13 | 1 | 13 | Jonesboro | Daniel Cabrera | P |
| 14 | 1 | 14 | Green Bay | John Baker | C |
| 15 | 1 | 15 | East Coast | Denard Span | OF |
| 16 | 1 | 16 | Gulf Breeze | Jed Lowrie | SS |
| 17 | 1 | 17 | Glab | Justin Masterson | P |
| 18 | 1 | 18 | Tidewater | Brad Ziegler | P |
| 19 | 1 | 19 | Freeport | Grant Balfour | P |
| 20 | 1 | 20 | Stamford | JP Howell | P |
| 21 | 1 | 21 | San Diego | Steven Straburg (prospect) |
P |
| 22 | 1 | 22 | Louisiana | Tommy Hanson (prospect) |
P |
| 23 | 1 | 23 | East Coast (from Mokena) |
Justin Smoak (prospect) |
1B |
| 24 | 1 | 24 | Westchester | Daniel Murphy | OF |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 25 | 2 | 1 | Beantown | Joe Inglett | 2B |
| 26 | 2 | 2 | Pike City | Brian Matusz (prospect) |
P |
| 27 | 2 | 3 | Buffalo | Edgar V. Gonzalez | 2B |
| 28 | 2 | 4 | Millers Tavern | James McDonald | P |
| 29 | 2 | 5 | Staten Island | Alcides Escobar | SS |
| 30 | 2 | 6 | Tampa | Joe Nelson | P |
| 31 | 2 | 7 | Arundel | Madison Bumgamer (prospect) |
P |
| 32 | 2 | 8 | Long Island | Matt Harrison | P |
| 33 | 2 | 9 | Turtle Beach | Corey Wade | P |
| 34 | 2 | 10 | Greensboro | Jorge Campillo | P |
| 35 | 2 | 11 | Arundel (from Baton Rouge) |
Jim Johnson | P |
| 36 | 2 | 12 | Chappaqua | Ramon Ramirez | P |
| 37 | 2 | 13 | Jonesboro | Scott Feldman | P |
| 38 | 2 | 14 | Green Bay | Jody Gerut | OF |
| 39 | 2 | 15 | Arundel (from East Coast) |
Matt Joyce | OF |
| 40 | 2 | 16 | Gulf Breeze | Nick Hundley | C |
| 41 | 2 | 17 | Glab | Jesse Carlson | P |
| 42 | 2 | 18 | Tidewater | Mike Adams | P |
| 43 | 2 | 19 | Freeport | Michael Bowden | P |
| 44 | 2 | 20 | Stamford | Steven Shell | P |
| 45 | 2 | 21 | San Diego | Dayan Viciedo (prospect) |
3B |
| 46 | 2 | 22 | Louisiana | Jesus Montero (prospect) |
C |
| 47 | 2 | 23 | Stamford (from Mokena) |
Fernando Tatis | OF |
| 48 | 2 | 24 | Westchester | Brett Anderson (prospect) |
P |
| Overall Pick |
Round number |
Pick number |
Player Selected | Pos | |
| 49 | 3 | 1 | Arundel (from Beantown) |
Martin Prado | 3B |
| 50 | 3 | 2 | Pike City | Max Ramirez | C |
| 51 | 3 | 3 | Buffalo | Odalis Perez | P |
| 52 | 3 | 4 | Millers Tavern | Aaron Cunningham | OF |
| 53 | 3 | 5 | Staten Island | Trevor Cahill (prospect) |
P |
| 54 | 3 | 6 | Tampa | Mat Gamel | 3B |
| 55 | 3 | 7 | Arundel | Jerry Hairston | OF |
| 56 | 3 | 8 | Long Island | Ryan Hanigan | C |
| 57 | 3 | 9 | Turtle Beach | Craig Breslow | P |
| 58 | 3 | 10 | Greensboro | Naftali Feliz (prospect) |
P |
| 59 | 3 | 11 | Baton Rouge | David Freese (prospect) |
3B |
| 60 | 3 | 12 | Chappaqua | Omar Infante | OF |
| 61 | 3 | 13 | Jonesboro | Brian Burres | P |
| 62 | 3 | 14 | Green Bay | Chris Dickerson | OF |
| 63 | 3 | 15 | East Coast | Chris Tillman (prospect) |
P |
| 64 | 3 | 16 | Gulf Breeze | John Grabow | P |
| 65 | 3 | 17 | Glab | J.A. Happ | P |
| 66 | 3 | 18 | Tidewater | Lars Anderson (prospect) |
1B |
| 67 | 3 | 19 | Tampa (from Freeport) |
Willy Aybar | 3B |
| 68 | 3 | 20 | Stamford | Ben Zobrist | SS |
| 69 | 3 | 21 | San Diego | Brian Buscher | 3B |
| 70 | 3 | 22 | Louisiana | Scott Lewis | P |
| 71 | 3 | 23 | Turtle Beach (from Mokena) |
Sergio Romo | P |
| 72 | 3 | 24 | Stamford (from Westchester) |
Emmanuel Burris | SS |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 73 | 4 | 1 | Beantown | Seth McClung | P |
| 74 | 4 | 2 | Pike City | Jonathon Niese | P |
| 75 | 4 | 3 | Buffalo | Jack Hannahan | 3B |
| 76 | 4 | 4 | Millers Tavern | Lou Marson | C |
| 77 | 4 | 5 | Staten Island | Mike Stanton (prospect) |
OF |
| 78 | 4 | 6 | Tampa | Clayton Richard | P |
| 79 | 4 | 7 | Arundel | Chan Ho Park | P |
| 80 | 4 | 8 | Long Island | Russ Branyan | 3B |
| 81 | 4 | 9 | Turtle Beach | John Jaso | C |
| 82 | 4 | 10 | Greensboro | Derek Holland (prospect) |
P |
| 83 | 4 | 11 | Baton Rouge | Joe Mather | OF |
| 84 | 4 | 12 | Baton Rouge (from Chappaqua) |
Jason Motte | P |
| 85 | 4 | 13 | Jonesboro | Gabe Kapler | OF |
| 86 | 4 | 14 | Green Bay | John Bowker | 1B |
| 87 | 4 | 15 | East Coast | Brett Gardner | OF |
| 88 | 4 | 16 | Gulf Breeze | Ray Durham | 2B |
| 89 | 4 | 17 | Glab | Kuii Uehrara (prospect) |
P |
| 90 | 4 | 18 | Tidewater | Tim Beckham (prospect) |
SS |
| 91 | 4 | 19 | Freeport | Brett Wallace (prospect) |
3B |
| 92 | 4 | 20 | Turtle Beach (from Stamford) |
Angel Salome | C |
| 93 | 4 | 21 | San Diego | Dallas McPherson | 3B |
| 94 | 4 | 22 | Louisiana | Joel Hanrahan | P |
| 95 | 4 | 23 | Turtle Beach (from Mokena) |
Carlos Santana (prospect) |
C |
| 96 | 4 | 24 | Westchester | Nick Evans | OF |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 97 | 5 | 1 | Beantown | Nick Masset | P |
| 98 | 5 | 2 | Pike City | Dave Ross | C |
| 99 | 5 | 3 | Buffalo | Gabe Gross | OF |
| 100 | 5 | 4 | Millers Tavern | Wladimir Balentien | OF |
| 101 | 5 | 5 | Staten Island | Josh Fields | 3B |
| 102 | 5 | 6 | Tampa | Jordan Zimmerman (prospect) |
P |
| 103 | 5 | 7 | Arundel | Jose Contreras | P |
| 104 | 5 | 8 | Long Island | David Purcey | P |
| 105 | 5 | 9 | Turtle Beach | Humberto Quintero | C |
| 106 | 5 | 10 | Greensboro | Mike Hampton | P |
| 107 | 5 | 11 | Baton Rouge | Luis Rodriguez | SS |
| 108 | 5 | 12 | Chappaqua | Buster Posey (prospect) |
C |
| 109 | 5 | 13 | Jonesboro | Will Nieves | C |
| 110 | 5 | 14 | Green Bay | John McDonald | SS |
| 111 | 5 | 15 | East Coast | Aquilino Lopez | P |
| 112 | 5 | 16 | Gulf Breeze | Clay Condrey | P |
| 113 | 5 | 17 | Glab | Roy Corcoran | P |
| 114 | 5 | 18 | Tidewater | Bill Bray | P |
| 115 | 5 | 19 | Freeport | Josh Geer | P |
| 116 | 5 | 20 | Stamford | Tim Alderson (prospect) |
P |
| 117 | 5 | 21 | Mokena (from San Diego) |
Angel Berroa | SS |
| 118 | 5 | 22 | Louisiana | Gaby Sanchez | 1B |
| 119 | 5 | 23 | Mokena | Brandon Boggs | OF |
| 120 | 5 | 24 | Westchester | Jerry Blevins | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 121 | 6 | 1 | Beantown | Jeremy Reed | OF |
| 122 | 6 | 2 | Pike City | Chris Getz | 2B |
| 123 | 6 | 3 | Buffalo | Sidney Ponson | P |
| 124 | 6 | 4 | Millers Tavern | Kila Ka'aihue | 1B |
| 125 | 6 | 5 | Staten Island | Bobby Parnell | P |
| 126 | 6 | 6 | Tampa | Jose Veras | P |
| 127 | 6 | 7 | Arundel | Arthur Rhodes | P |
| 128 | 6 | 8 | Long Island | Yonder Alonso (prospect) |
1B |
| 129 | 6 | 9 | Turtle Beach | Jhoulys Chacin (prospect) |
P |
| 130 | 6 | 10 | Greensboro | Willie Bloomquist | OF |
| 131 | 6 | 11 | Baton Rouge | Shawn Riggans | C |
| 132 | 6 | 12 | Chappaqua | Travis Ishikawa | 1B |
| 133 | 6 | 13 | Jonesboro | Saul Rivera | P |
| 134 | 6 | 14 | Green Bay | Keiichi Yabu | P |
| 135 | 6 | 15 | East Coast | Scott Schoeneweis | P |
| 136 | 6 | 16 | Gulf Breeze | Jeff Larish | 3B |
| 137 | 6 | 17 | Glab | Jeff Francis | P |
| 138 | 6 | 18 | Tidewater | Kevin Correia | P |
| 139 | 6 | 19 | Freeport | Doug Waechter | P |
| 140 | 6 | 20 | Westchester (from Stamford) |
Kyle McClellan | P |
| 141 | 6 | 21 | San Diego | Stephen Holm | C |
| 142 | 6 | 22 | Louisiana | Ryan Tucker | P |
| 143 | 6 | 23 | Stamford (from Mokena) |
Alex Hinshaw | P |
| 144 | 6 | 24 | Westchester | Cale Iorg (prospect) |
SS |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 145 | 7 | 1 | Beantown | Ramon Santiago | SS |
| 146 | 7 | 2 | Louisiana (from Pike City) |
Alfredo Aceves | P |
| 147 | 7 | 3 | Buffalo | Jose Vidro | 1B |
| 148 | 7 | 4 | Millers Tavern | Logan Morrison (prospect) |
1B |
| 149 | 7 | 5 | Staten Island | Eddie Kunz | P |
| 150 | 7 | 6 | Freeport (from Tampa) |
Garrett Mock | P |
| 151 | 7 | 7 | Arundel | Phil Coke | P |
| 152 | 7 | 8 | Long Island | Cesar Jimenez | P |
| 153 | 7 | 9 | Mokena (from Turtle Beach) |
Jason Michaels | OF |
| 154 | 7 | 10 | Greensboro | Jeff Karstens | P |
| 155 | 7 | 11 | Baton Rouge | Brendan Ryan | SS |
| 156 | 7 | 12 | Chappaqua | Brian Anderson | OF |
| 157 | 7 | 13 | Jonesboro | R.A. Dickey | P |
| 158 | 7 | 14 | Green Bay | Tony Pena | P |
| 159 | 7 | 15 | East Coast | Franklyn German | P |
| 160 | 7 | 16 | Gulf Breeze | Kenshin Kawakami (prospect) |
P |
| 161 | 7 | 17 | Staten Island (from Glab) |
Luis Valbuena | 2B |
| 162 | 7 | 18 | Tidewater | Phil Dumatrait | P |
| 163 | 7 | 19 | Freeport | Andruw Jones | OF |
| 164 | 7 | 20 | Stamford | Eric Stults | P |
| 165 | 7 | 21 | San Diego | Dusty Ryan | C |
| 166 | 7 | 22 | Louisiana | Ramon A Ramirez | P |
| 167 | 7 | 23 | Mokena | Brad Wilkerson | OF |
| 168 | 7 | 24 | Westchester | Cliff Pennington | 2B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 169 | 8 | 1 | Beantown | Brandon Snyder (prospect) |
1B |
| 170 | 8 | 2 | Pike City | Jake Arrieta (prospect) |
P |
| 171 | 8 | 3 | Buffalo | Waiver loss | |
| 172 | 8 | 4 | Millers Tavern | Kam Mickolio | P |
| 173 | 8 | 5 | Staten Island | Jimmy Barthmeier | P |
| 174 | 8 | 6 | Tampa | Gordon Beckham (prospect) |
SS |
| 175 | 8 | 7 | Arundel | Waiver loss | |
| 176 | 8 | 8 | Long Island | Jorge Julio | P |
| 177 | 8 | 9 | Mokena (from Turtle Beach) |
Omar Quintanilla | 2B |
| 178 | 8 | 10 | Greensboro | Dustin Nippert | P |
| 179 | 8 | 11 | Baton Rouge | Glendon Rusch | P |
| 180 | 8 | 12 | Chappaqua | Nolan Reimold (prospect) |
OF |
| 181 | 8 | 13 | Jonesboro | Kevin Cash | C |
| 182 | 8 | 14 | Green Bay | Greg Norton | OF |
| 183 | 8 | 15 | Mokena (from East Coast) |
Logan Kensing | P |
| 184 | 8 | 16 | Gulf Breeze | Brian Barton | OF |
| 185 | 8 | 17 | Glab | Waiver loss | |
| 186 | 8 | 18 | Tidewater | Will Venable | OF |
| 187 | 8 | 19 | Freeport | Raul Chavez | C |
| 188 | 8 | 20 | Stamford | Waiver loss | |
| 189 | 8 | 21 | San Diego | Dennis Sarfate | P |
| 190 | 8 | 22 | Louisiana | Matt Tolbert | 3B |
| 191 | 8 | 23 | Freeport (from Mokena) |
Freddy Dolsi | P |
| 192 | 8 | 24 | Westchester | Renyel Pinto | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 193 | 9 | 1 | Greensboro (from Beantown) |
Anderson Hernandez | 2B |
| 194 | 9 | 2 | Pike City | Matt Tuiasosopo | 3B |
| 195 | 9 | 3 | Buffalo | Brian Bass | P |
| 196 | 9 | 4 | Millers Tavern | Josh Outman | P |
| 197 | 9 | 5 | Staten Island | Boone Logan | P |
| 198 | 9 | 6 | Tampa | Toby Hall | C |
| 199 | 9 | 7 | Arundel | Ramon Troncoso | P |
| 200 | 9 | 8 | Long Island | Carl Pavano | P |
| 201 | 9 | 9 | Turtle Beach | Ryan Perry (prospect) |
P |
| 202 | 9 | 10 | Greensboro | Micah Hoffpauir | OF |
| 203 | 9 | 11 | Baton Rouge | Sean Green | P |
| 204 | 9 | 12 | Chappaqua | Fernando Perez | OF |
| 205 | 9 | 13 | Jonesboro | Josh Banks | P |
| 206 | 9 | 14 | Green Bay | Eric Bruntlett | OF |
| 207 | 9 | 15 | East Coast | Mike Hinckley | P |
| 208 | 9 | 16 | Gulf Breeze | Michael Barrett | C |
| 209 | 9 | 17 | Glab | Guillermo Mota | P |
| 210 | 9 | 18 | Tidewater | Sean Rodriguez | 2B |
| 211 | 9 | 19 | Freeport | Andrew Carignan (prospect) |
P |
| 212 | 9 | 20 | Stamford | Ben Revere (prospect) |
IF |
| 213 | 9 | 21 | San Diego | George Kottaras | C |
| 214 | 9 | 22 | Louisiana | Jose Mijares | P |
| 215 | 9 | 23 | Mokena | Chris Burke | OF |
| 216 | 9 | 24 | Westchester | Jason Frasor | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 217 | 10 | 1 | Beantown | Jason Castro (prospect) |
C |
| 218 | 10 | 2 | Pike City | Shawn Camp | P |
| 219 | 10 | 3 | Buffalo | Fu-Te Ni (prospect) |
P |
| 220 | 10 | 4 | Millers Tavern | Tyler Flowers (prospect) |
C |
| 221 | 10 | 5 | Staten Island | Jamie Burke | C |
| 222 | 10 | 6 | Tampa | Joaquin Arias | 2B |
| 223 | 10 | 7 | Westchester (from Arundel) |
Brayan Pena | C |
| 224 | 10 | 8 | Long Island | Mike Rivera | C |
| 225 | 10 | 9 | Stamford (from Turtle Beach) |
Lou Montanez | OF |
| 226 | 10 | 10 | Greensboro | Ryan Shealy | 1B |
| 227 | 10 | 11 | Baton Rouge | Jamey Wright | P |
| 228 | 10 | 12 | Chappaqua | Bryan LaHair | 1B |
| 229 | 10 | 13 | Jonesboro | Pass | |
| 230 | 10 | 14 | Green Bay | Guillermo Quiroz | C |
| 231 | 10 | 15 | East Coast | Mike Lincoln | P |
| 232 | 10 | 16 | Gulf Breeze | J.P.Arencibia (prospect) |
C |
| 233 | 10 | 17 | Glab | Jason Donald (prospect) |
2B |
| 234 | 10 | 18 | Tidewater | Charlie Morton | P |
| 235 | 10 | 19 | Freeport | Pass | |
| 236 | 10 | 20 | Stamford | Brett Cecil (prospect) |
P |
| 237 | 10 | 21 | Chappaqua (from San Diego) |
Paul Hoover | C |
| 238 | 10 | 22 | Louisiana | German Duran | 3B |
| 239 | 10 | 23 | Mokena | Josh Fields (prospect) |
P |
| 240 | 10 | 24 | Westchester | Austin Romine (prospect) |
C |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 241 | 11 | 1 | Beantown | Alex Cintron | SS |
| 242 | 11 | 2 | Pike City | Pass | |
| 243 | 11 | 3 | Buffalo | Eric Hosmer (prospect) |
1B |
| 244 | 11 | 4 | Millers Tavern | Francisco Cervelli | C |
| 245 | 11 | 5 | Staten Island | Pass | |
| 246 | 11 | 6 | Tampa | Julio Borbon (prospect) |
OF |
| 247 | 11 | 7 | Turtle Beach |
Pass | |
| 248 | 11 | 8 | Long Island | Jeremy Hellickson (prospect) |
P |
| 249 | 11 | 9 | Turtle Beach | Pass | |
| 250 | 11 | 10 | Greensboro | Don Giese | P |
| 251 | 11 | 11 | Baton Rouge | Pass | |
| 252 | 11 | 12 | Arundel (from Pike City through Chappaqua) |
Grant Geen (prospect) |
SS |
| 253 | 11 | 13 | Jonesboro | Brian Stokes | P |
| 254 | 11 | 14 | Green Bay | David Huff (prospect) |
P |
| 255 | 11 | 15 | East Coast | Pass | |
| 256 | 11 | 16 | Gulf Breeze | Mike MacDougal | P |
| 257 | 11 | 17 | Glab | Mike Rabelo | C |
| 258 | 11 | 18 | Tidewater | Chris Waters | P |
| 259 | 11 | 19 | Freeport | Pass | |
| 260 | 11 | 20 | Stamford | Kyle Skipworth (prospect) |
C |
| 261 | 11 | 21 | San Diego | Greg Reynolds | P |
| 262 | 11 | 22 | Louisiana | Conor Gillaspie | 3B |
| 263 | 11 | 23 | Mokena | Daniel Moskos (prospect) |
P |
| 264 | 11 | 24 | Westchester | Billy Buckner | P |
|
|
|
|
|
|
| XTR | 1 | Buffalo | Mark Lowe | P | |
| XTR | 2 | Arundel | Adam Melhuse | C | |
| XTR | 3 | Glab | Luis Rivas | SS | |
| XTR | 4 | Stamford | Chad Moeller | C |