| POS | ROUND ONE | SELECTION | POS | ROUND TWO | SELECTION | POS | ROUND THREE | SELECTION |
| 1 | Des Moines | Evan Longoria | 25 | Sacramento (DES) | Jed Lowrie | 49 | Charlotte (DES) | Mike Adams |
| 2 | New York (CHA) | Clayton Kershaw | 26 | Charlotte | Nick Adenhart | 50 | Charlotte | Ben Zobrist |
| 3 | Hartford (KCK) | David Price | 27 | Berlin | Gaby Sanchez | 51 | King County | J A Happ |
| 4 | Berlin | Max Scherzer | 28 | Hartford (KCK) | Mike Aviles | 52 | Berlin | Max Ramirez |
| 5 | Worcester (NY) | Jay Bruce | 29 | New York | Jeff Samardzija | 53 | Charlotte (NY) | Dennys Reyes |
| 6 | Sacramento | Chris Davis | 30 | Buffalo | Brian Giles | 54 | Sacramento | Scott Elbert |
| 7 | Buffalo | Armando Galarraga | 31 | Sacramento | Angel Salome | 55 | Buffalo | Jim Johnson |
| 8 | Manchester | Travis Snider | 32 | Manchester | Jorge Campillo | 56 | Manchester | Ramon Ramirez |
| 9 | Hartford | Alexei Ramirez | 33 | Hartford | Grant Balfour | 57 | Hartford | Chris Perez |
| 10 | Boston College | Greg Smith | 34 | Manorville | Ryan Tucker | 58 | Charlotte (BCE) | Craig Breslow |
| 11 | Manorville | Johnny Cueto | 35 | Boston College | Cory Wade | 59 | Manorville | Daniel Murphy |
| 12 | Lake Norman | Hiroki Kuroda | 36 | Grand Haven (LNY) | John Jaso | 60 | Lake Norman | Sergio Romo |
| 13 | Sacramento (TAL) | Mat Gamel | 37 | Sacramento (TAL) | Alcides Escobar | 61 | Sacramento (TAL) | James McDonald |
| 14 | Tacoma | Chris Volstad | 38 | Tacoma | Emmanuel Burriss | 62 | Tacoma | Gregor Blanco |
| 15 | Denver | Carlos Gonzalez | 39 | Denver | Radhames Liz | 63 | Denver | Travis Ishikawa |
| 16 | Grand Haven | Dexter Fowler | 40 | Grand Haven | Matt Joyce | 64 | Grand Haven | Matt Antonelli |
| 17 | Winter Hill | Pablo Sandoval | 41 | Charlotte (MIL) | John Baker | 65 | Winter Hill | Jonathan Niese |
| 18 | Boston Coll (MIL) | Justin Masterson | 42 | Winter Hill | Lou Marson | 66 | Emerald City (MIL) | Jason Giambi |
| 19 | Lynnwood | Jose Arredondo | 43 | Orange County | Jesse Carlson | 67 | Lynnwood | Jerry Hairston |
| 20 | Boothbay (OCC) | Taylor Teagarden | 44 | Worcester (LYN) | Nelson Cruz | 68 | Orange County | Nick Hundley |
| 21 | Worcester | Denard Span | 45 | Worcester | Jason Motte | 69 | Lynnwood (WOR) | Chan Ho Park |
| 22 | Emerald City | Michael Bowden | 46 | Emerald City | Blake DeWitt | 70 | Emerald City | Matt Harrison |
| 23 | Plainfield | Brad Ziegler | 47 | Plainfield | Chris Dickerson | 71 | Plainfield | Willie Aybar |
| 24 | Hartford (BHL) | Gio Gonzalez | 48 | Boothbay | Jody Gerut | 72 | Hartford (BHL) | Jorge de la Rosa |
| POS | ROUND FOUR | SELECTION | POS | ROUND FIVE | SELECTION | POS | ROUND SIX | SELECTION |
| 73 | Charlotte (DES) | Steven Shell | 97 | Des Moines | Brian Buscher | 121 | Des Moines | Merkin Valdez |
| 74 | Charlotte | Clint Barmes | 98 | Charlotte | Clayton Richard | 122 | Charlotte | Micah Hoffpauir |
| 75 | Des Moines (BER) | Jerry Blevins | 99 | King County | Fernando Perez | 123 | Berlin | Roger Bernadina |
| 76 | King County | Russell Branyan | 100 | Berlin | Kila Ka'aihue | 124 | King County | Conor Gillaspie |
| 77 | New York | Jeff Niemann | 101 | New York | Brent Lillibridge | 125 | New York | Jose Mijares |
| 78 | Buffalo | John Grabow | 102 | Sacramento | Kosuke Fukudome | 126 | Buffalo | Roy Corcoran |
| 79 | Sacramento | Reid Brignac | 103 | Buffalo | Joe Inglett | 127 | Sacramento | Carl Pavano |
| 80 | Manchester | Joe Nelson | 104 | Manchester | Fernando Tatis | 128 | Manchester | Scott Schoenweis |
| 81 | Hartford | Pedro Martinez | 105 | Hartford | Kevin Millar | 129 | Hartford | Kevin Cash |
| 82 | Manorville | Sean Rodriguez | 106 | Boston College | Phil Coke | 130 | Manorville | Kameron Mickolio |
| 83 | Boston College | Jose Contreras | 107 | Des Moines (MAN) | Will Venable | 131 | Boston College | Mike Hinckley |
| 84 | King County (LNY) | Eric Hurley | 108 | Lake Norman | Doug Waechter | 132 | Lake Norman | Alex Hinshaw |
| 85 | Sacramento (TAL) | Tommy Hunter | 109 | Tallahassee | Gabe Kapler | 133 | Tallahassee | Ramon Castro |
| 86 | Tacoma | Keichi Yabu | 110 | Tacoma | Eddie Guardado | 134 | Tacoma | Jack Hannahan |
| 87 | Lynnwood (DEN) | Scott Lewis | 111 | Denver | Solomon Torres | 135 | Denver | Jose Veras |
| 88 | Grand Haven | Colin Balester | 112 | Grand Haven | Kyle McClellan | 136 | Grand Haven | David Purcey |
| 89 | Boston Coll (MIL) | Aaron Cunningham | 113 | Winter Hill | Henry Blanco | 137 | Emerald City (MIL) | Aquilino Lopez |
| 90 | Winter Hill | Odalis Perez | 114 | Worcester (MIL) | Josh Bard | 138 | Winter Hill | Humberto Quintero |
| 91 | Orange County | Brandon McCarthy | 115 | Lynnwood | Jeff Larish | 139 | Orange County | Alfredo Aceves |
| 92 | Lynnwood | Arthur Rhodes | 116 | Orange County | Lou Montanez | 140 | Denver (LYN) | Jorge Julio |
| 93 | Charlotte (WOR) | Ramon A Ramirez | 117 | Worcester | Rafael Soriano | 141 | Worcester | Edgar V Gonzalez |
| 94 | Emerald City | Garrett Mock | 118 | Emerald City | DJ Carrasco | 142 | Hartford (ECW) | Brian Stokes |
| 95 | Plainfield | Joe Mather | 119 | Plainfield | Raul Chavez | 143 | Plainfield | Ryan Shealy |
| 96 | Boothbay | Dan Giese | 120 | Hartford (BHL) | Mark Hendrickson | 144 | Boothbay | Cody Ransom |
| POS | ROUND SEVEN | SELECTION | POS | ROUND EIGHT | SELECTION | POS | ROUND NINE | SELECTION |
| 145 | Des Moines | Eugenio Velez | 169 | Des Moines | Duaner Sanchez | 188 | Des Moines | Michael Hollimon |
| 146 | New York (CHA) | Wilson Betemit | 170 | King County | Jonathan Meloan | 189 | King County | Pat Neshek |
| 147 | King County | Eric Chavez | 171 | New York | Carlos Rosa | 190 | New York | Greg Golson |
| 148 | Berlin | Clint Sammons | 172 | Buffalo | Wil Nieves | 191 | Sacramento | Jeremy Reed |
| 149 | New York | David Robertson | 173 | Sacramento | Kevin Frandsen | 192 | Buffalo | Danny Ardoin |
| 150 | Sacramento | Nate Robertson | 174 | Manchester | Bobby Parnell | 193 | Manchester | Adam Melhuse |
| 151 | Buffalo | Scott Feldman | 175 | Hartford | Mitch Stetter | 194 | Hartford | Brendon Ryan |
| 152 | Manchester | Dennis Sarfate | 176 | Manorville | Jeremy Accardo | 195 | Manorville | David Aardsma |
| 153 | Hartford | Wes Helms | 177 | Lake Norman | Brandon Boggs | 196 | Lake Norman | Lance Cormier |
| 154 | Boston College | Nick Evans | 178 | Tallahassee | Scott Eyre | 197 | Tallahassee | Peter Moylan |
| 155 | Manorville | Ramon Troncoso | 179 | Tacoma | Brian Barton | 198 | Tacoma | Chad Cordero |
| 156 | Lake Norman | John Bowker | 180 | Milford | Adam Everett | 199 | Grand Haven | Daniel Ray Herrera |
| 157 | Tallahassee | Greg Norton | 181 | Winter Hill | Mitch Talbot | 200 | Grand Haven | Humberto Sanchez |
| 158 | Tacoma | Wesley Wright | 182 | Orange County | Brett Gardner | 201 | Winter Hill | Charlie Morton |
| 159 | Denver | Wil Ledezma | 183 | Lynnwood | Travis Metcalf | 202 | Worcester (MIL) | Michael Barrett |
| 160 | Grand Haven | Adam Rosales | 184 | Emerald City (WOR) | Shairon Martis | 203 | Lynnwood | Josh Whitesell |
| 161 | Winter Hill | Josh Outman | 185 | Emerald City | Mark Mulder | 204 | Orange County | Matt Tuiasasopo |
| 162 | Worcester (MIL) | Jamie Garcia | 186 | Plainfield | John McDonald | 205 | Worcester | Brandon Lyon |
| 163 | Lynnwood | Anderson Hernandez | 187 | Boothbay | Brad Nelson | 206 | Milford (ECW) | Franklyn German |
| 164 | Orange County | Chris Getz | 207 | Plainfield | Oscar Salazar | |||
| 165 | Worcester | Cla Meredith | 208 | Boothbay | German Duran | |||
| 166 | Emerald City | Josh Geer | ||||||
| 167 | Plainfield | Dusty Ryan | ||||||
| 168 | Boothbay | Cesar Jimenez | ||||||
| POS | ROUND TEN | SELECTION | POS | ROUND ELEVEN | SELECTION | POS | ROUND TWELVE | SELECTION |
| 209 | Des Moines | Mark DiFelice | 226 | Des Moines | Juan Morillo | 242 | Des Moines | Jason Hirsh |
| 210 | King County | Mike Rivera | 227 | Sacramento | Jeff Baisley | 243 | Buffalo | TJ Beam |
| 211 | Buffalo | Guillermo Mota | 228 | Buffalo | David Dellucci | 244 | Sacramento | Daryl Thompson |
| 212 | Sacramento | Matt Diaz | 229 | Manchester | Cliff Pennington | 245 | Manchester | Josh Banks |
| 213 | Manchester | Chris Duncan | 230 | Hartford | Keith Foulke | 246 | Hartford | Norris Hopper |
| 214 | King County (HAR) | Josh Roenicke | 231 | Manorville | Tyler Clippard | 247 | Manorville | Matt Murton |
| 215 | Manorville | Shawn Riggans | 232 | Lake Norman | Joachin Arias | 248 | Lake Norman | Rob Bowen |
| 216 | Lake Norman | Corey Patterson | 233 | Tallahassee | Shawn Camp | 249 | Tacoma | Nick Masset |
| 217 | Tallahassee | Moises Alou | 234 | Tacoma | Michael Aubrey | 250 | Milford | Steve Holm |
| 218 | Tacoma | Mike Lincoln | 235 | Winter Hill | Francisco Cervelli | 251 | Lynnwood | Jeff Bailey |
| 219 | Milford | Billy Sadler | 236 | Milford | R A Dickey | 252 | Charlotte (WOR) | Miguel Cairo |
| 220 | Winter Hill | Mitchell Boggs | 237 | Lynnwood | Ryan Speier | 253 | Boothbay | Kevin Jepsen |
| 221 | Lynnwood | Wade LeBlanc | 238 | Orange County | Brian LaHair | |||
| 222 | Orange County | Ryan Hanigan | 239 | Charlotte (WOR) | Lance Broadway | |||
| 223 | Worcester | Boof Bonser | 240 | Emerald City | Evan Meek | |||
| 224 | Emerald City | Mike Rabelo | 241 | Boothbay | Kei Igawa | |||
| 225 | Boothbay | Matt Macri | ||||||
| POS | ROUND THIRTEEN | SELECTION | POS | ROUND FOURTEEN | SELECTION | POS | ROUND FIFTEEN | SELECTION |
| 254 | Des Moines | Neal Cotts | 264 | Buffalo | Jose Vidro | 271 | Sacramento | Justin Speier |
| 255 | Sacramento | Jason Michaels | 265 | Sacramento | Bobby Howry | 272 | Hartford | Frank Thomas |
| 256 | Buffalo | Robinzon Diaz | 266 | Hartford | Clete Thomas | 273 | Lynnwood (MIL) | Luke Montz |
| 257 | Manchester | Delwyn Young | 267 | Lake Norman | Ryan Raburn | 274 | Worcester | Aaron Boone |
| 258 | Hartford | Phil Dumatrait | 268 | Milford | Mike MacDougal | 275 | Hartford (BHL) | Angel Pagan |
| 259 | Lake Norman | John Parrish | 269 | Worcester | Ron Villone | |||
| 260 | Tacoma | Chad Reineke | 270 | Boothbay | Warner Madrigal | |||
| 261 | Milford | Chris Waters | ||||||
| 262 | Worcester | Josh Rupe | ||||||
| 263 | Boothbay | Chris Carter | ||||||
| POS | ROUND SIXTEEN | SELECTION | POS | ROUND SEVENTEEN | SELECTION | |||
| 276 | Sacramento | Rick Vanden Hurk | 279 | Worcester | Sidney Ponson | |||
| 277 | Hartford | Tom Gordon | ||||||
| 278 | Milford (WOR) | Dustin Moseley | ||||||