2006 Draft Results
| Pick | Round | RdPk | Team | pick |
| 1 | 13 | 1 | Santa Clara Leopardos | Cole Hamels |
| 2 | 13 | 2 | Bocomo Blues | Delmon Young |
| 3 | 13 | 3 | Galway Galleons | Jered Weaver |
| 4 | 13 | 4 | Carolina Sandlappers | Stephen Drew |
| 5 | 13 | 5 | Bellingham Pilots | Jason Jennings |
| 6 | 13 | 6 | Detroit Wheels | Dan Uggla |
| 7 | 13 | 7 | Nashua Nonames | Howie Kendrick |
| 8 | 13 | 8 | Binghamton Senators | Joel Zumaya |
| 9 | 13 | 9 | Maui Stingrays | Anibal Sanchez |
| 10 | 13 | 10 | Camano Island Wormburners | Josh Barfield |
| 11 | 13 | 11 | New Jersey Patriots | Michael Cuddyer |
| 12 | 13 | 12 | Santa Clara Leopardos | Nick Markakis |
| 13 | 13 | 13 | Duluth Dukes | Russ Martin |
| 14 | 13 | 14 | Rosehaven River Dogs | Aaron Cook |
| 15 | 13 | 15 | Charlotte Knights | Ian Snell |
| 16 | 13 | 16 | Madiba United | Carlos Quentin |
| 17 | 13 | 17 | Tampa Bay Pirates | Adam LaRoche |
| 18 | 13 | 18 | New Orleans Pelicans | Matt Garza |
| 19 | 13 | 19 | Nashua Nonames | Chris Iannetta |
| 20 | 13 | 20 | Mystic Sea Horses | Kenji Johjima |
| 21 | 13 | 21 | Kissimmee Cardinals | Chad Billingsley |
| 22 | 13 | 22 | Hollywood Heat | Gary Matthews |
| 23 | 13 | 23 | Scottsdale Cougars | Nomar Garciaparra |
| 24 | 13 | 24 | Dresden Blacks | Mark Teahen |
| 25 | 13 | 25 | Seoul Fighters | Ian Kinsler |
| 26 | 13 | 26 | Cambridge Longfellows | Nate Robertson |
| 27 | 14 | 1 | New Orleans Pelicans | Chris B. Young |
| 28 | 14 | 2 | Charlotte Knights | John Maine |
| 29 | 14 | 3 | Rosehaven River Dogs | Gil Meche |
| 30 | 14 | 4 | Rosehaven River Dogs | Jason Kendall |
| 31 | 14 | 5 | New Jersey Patriots | Andre Ethier |
| 32 | 14 | 6 | Nashua Nonames | Jeremy Sowers |
| 33 | 14 | 7 | Binghamton Senators | Boof Bonser |
| 34 | 14 | 8 | Bellingham Pilots | Jonathan Broxton |
| 35 | 14 | 9 | Maui Stingrays | Juan Rivera |
| 36 | 14 | 10 | Carolina Sandlappers | Melky Cabrera |
| 37 | 14 | 11 | Galway Galleons | James Shields |
| 38 | 14 | 12 | Carolina Sandlappers | Ty Wigginton |
| 39 | 14 | 13 | Kissimmee Cardinals | Craig Monroe |
| 40 | 14 | 14 | Cambridge Longfellows | Mark DeRosa |
| 41 | 14 | 15 | Scottsdale Cougars | Jacque Jones |
| 42 | 15 | 1 | New Orleans Pelicans | Jon Lester |
| 43 | 15 | 2 | Charlotte Knights | Jason Bartlett |
| 44 | 15 | 3 | Rosehaven River Dogs | Jamie Moyer |
| 45 | 15 | 4 | Tampa Bay Pirates | Eric Byrnes |
| 46 | 15 | 5 | Duluth Dukes | Claudio Vargas |
| 47 | 15 | 6 | New Jersey Patriots | Chris Duncan |
| 48 | 15 | 7 | Nashua Nonames | Adam Loewen |
| 49 | 15 | 8 | Binghamton Senators | Mark Hendrickson |
| 50 | 15 | 9 | Bellingham Pilots | Orlando Hernandez |
| 51 | 15 | 10 | Maui Stingrays | Johnny Estrada |
| 52 | 15 | 11 | Detroit Wheels | Rich Aurilia |
| 53 | 15 | 12 | Carolina Sandlappers | Matt Murton |
| 54 | 15 | 13 | Galway Galleons | J.J. Putz |
| 55 | 15 | 14 | Detroit Wheels | Mike Pelfrey |
| 56 | 15 | 15 | Bocomo Blues | Chris Burke |
| 57 | 15 | 16 | Camano Island Wormburners | Takashi Saito |
| 58 | 15 | 17 | Kissimmee Cardinals | Juan Cruz |
| 59 | 15 | 18 | Hollywood Heat | Marcus Thames |
| 60 | 15 | 19 | Santa Clara Leopardos | Esteban Loaiza |
| 61 | 15 | 20 | Cambridge Longfellows | Cla Meredith |
| 62 | 16 | 1 | New Orleans Pelicans | Corey Patterson |
| 63 | 16 | 2 | Dresden Blacks | Josh Bard |
| 64 | 16 | 3 | Madiba United | Ricky Nolasco |
| 65 | 16 | 4 | Rosehaven River Dogs | Emil Brown |
| 66 | 16 | 5 | Tampa Bay Pirates | Pedro Feliz |
| 67 | 16 | 6 | Washington Grays | Akinori Otsuka |
| 68 | 16 | 7 | New Jersey Patriots | Woody Williams |
| 69 | 16 | 8 | Camano Island Wormburners | Joe Beimel |
| 70 | 16 | 9 | Binghamton Senators | Macier Izturis |
| 71 | 16 | 10 | Bellingham Pilots | Dave Roberts |
| 72 | 16 | 11 | Maui Stingrays | Jaret Wright |
| 73 | 16 | 12 | Washington Grays | Dennys Reyes |
| 74 | 16 | 13 | Carolina Sandlappers | Mike Gonzalez |
| 75 | 16 | 14 | Galway Galleons | Gerald Laird |
| 76 | 16 | 15 | Washington Grays | Eric Milton |
| 77 | 16 | 16 | Bocomo Blues | Sean Marshall |
| 78 | 16 | 17 | Camano Island Wormburners | Dan Wheeler |
| 79 | 16 | 18 | Kissimmee Cardinals | Kevin Kouzmanoff |
| 80 | 16 | 19 | Hollywood Heat | Scott Proctor |
| 81 | 16 | 20 | Scottsdale Cougars | Justin Duchscherer |
| 82 | 16 | 21 | Cambridge Longfellows | Luke Scott |
| 83 | 17 | 1 | New Orleans Pelicans | Pedro Feliciano |
| 84 | 17 | 2 | Charlotte Knights | Joe Borowski |
| 85 | 17 | 3 | Madiba United | David Ross |
| 86 | 17 | 4 | Rosehaven River Dogs | Jorge Julio |
| 87 | 17 | 5 | Tampa Bay Pirates | Matt Capps |
| 88 | 17 | 6 | Duluth Dukes | Matt Diaz |
| 89 | 17 | 7 | New Jersey Patriots | Chad Qualls |
| 90 | 17 | 8 | Texas Lightning | Shea Hillenbrand |
| 91 | 17 | 9 | Santa Clara Leopardos | Jamey Carroll |
| 92 | 17 | 10 | Binghamton Senators | Enrique Gonzalez |
| 93 | 17 | 11 | Bellingham Pilots | Kenny Lofton |
| 94 | 17 | 12 | Maui Stingrays | Taylor Buchholz |
| 95 | 17 | 13 | Detroit Wheels | Salomon Torres |
| 96 | 17 | 14 | Carolina Sandlappers | Joaquin Benoit |
| 97 | 17 | 15 | Galway Galleons | Gabe Gross |
| 98 | 17 | 16 | Washington Grays | Hector Carrasco |
| 99 | 17 | 17 | Bocomo Blues | Casey Janssen |
| 100 | 17 | 18 | Camano Island Wormburners | Andrew Miller |
| 101 | 17 | 19 | Kissimmee Cardinals | Miguel Olivo |
| 102 | 17 | 20 | Hollywood Heat | Darren Oliver |
| 103 | 17 | 21 | Scottsdale Cougars | Nick Punto |
| 104 | 17 | 22 | Cambridge Longfellows | James Loney |
| 105 | 17 | 23 | New Orleans Pelicans | Joe Saunders |
| 106 | 18 | 1 | Charlotte Knights | Ramon Ortiz |
| 107 | 18 | 2 | Madiba United | Ryan Shealy |
| 108 | 18 | 3 | Rosehaven River Dogs | Geoff Geary |
| 109 | 18 | 4 | Tampa Bay Pirates | Bob Wickman |
| 110 | 18 | 5 | Duluth Dukes | Josh Fogg |
| 111 | 18 | 6 | New Jersey Patriots | Chad Bradford |
| 112 | 18 | 7 | Nashua Nonames | Mike Napoli |
| 113 | 18 | 8 | Santa Clara Leopardos | Lastings Milledge |
| 114 | 18 | 9 | Binghamton Senators | Jeff Davanon |
| 115 | 18 | 10 | Bellingham Pilots | Jose Valentin |
| 116 | 18 | 11 | Maui Stingrays | Endy Chavez |
| 117 | 18 | 12 | Detroit Wheels | Will Ohman |
| 118 | 18 | 13 | Carolina Sandlappers | Geoff Zaun |
| 119 | 18 | 14 | Galway Galleons | Jesse Crain |
| 120 | 18 | 15 | Washington Grays | Troy Tulowitzki |
| 121 | 18 | 16 | Bocomo Blues | Todd Jones |
| 122 | 18 | 17 | Camano Island Wormburners | Oscar Villareal |
| 123 | 18 | 18 | Kissimmee Cardinals | Kyle Farnsworth |
| 124 | 18 | 19 | Hollywood Heat | Fernando Nieve |
| 125 | 18 | 20 | Scottsdale Cougars | Matt Thornton |
| 126 | 18 | 21 | Dresden Blacks | Jon Rauch |
| 127 | 18 | 22 | Cambridge Longfellows | Brandon League |
| 128 | 19 | 1 | New Orleans Pelicans | Matt Kemp |
| 129 | 19 | 2 | Charlotte Knights | John Buck |
| 130 | 19 | 3 | Madiba United | Scott Linebrink |
| 131 | 19 | 4 | Rosehaven River Dogs | Steve Trachsel |
| 132 | 19 | 5 | Tampa Bay Pirates | Aaron Sele |
| 133 | 19 | 6 | Duluth Dukes | Jay Payton |
| 134 | 19 | 7 | New Jersey Patriots | Tim Corcoran |
| 135 | 19 | 8 | Nashua Nonames | Hong-Chih Kuo |
| 136 | 19 | 9 | Santa Clara Leopardos | Scott Downs |
| 137 | 19 | 10 | Binghamton Senators | Alex Cintron |
| 138 | 19 | 11 | Bellingham Pilots | Scott Spiezio |
| 139 | 19 | 12 | Maui Stingrays | Esteban German |
| 140 | 19 | 13 | Detroit Wheels | Tony Graffanino |
| 141 | 19 | 14 | Carolina Sandlappers | Rafael Betancourt |
| 142 | 19 | 15 | Galway Galleons | Jose Bautista |
| 143 | 19 | 16 | Washington Grays | Mike Lamb |
| 144 | 19 | 17 | Bocomo Blues | Mike Piazza |
| 145 | 19 | 18 | Camano Island Wormburners | Rodrigo Lopez |
| 146 | 19 | 19 | Kissimmee Cardinals | Mike Thompson |
| 147 | 19 | 20 | Hollywood Heat | Jason Hirsh |
| 148 | 19 | 21 | Scottsdale Cougars | Alan Embree |
| 149 | 19 | 22 | Dresden Blacks | Frank Thomas |
| 150 | 19 | 23 | Cambridge Longfellows | Trever Miller |
| 151 | 20 | 1 | New Orleans Pelicans | Luke Hudson |
| 152 | 20 | 2 | Charlotte Knights | David Weathers |
| 153 | 20 | 3 | Madiba United | Ramon Ramirez |
| 154 | 20 | 4 | Rosehaven River Dogs | Shane Victorino |
| 155 | 20 | 5 | Tampa Bay Pirates | Brad Hennessey |
| 156 | 20 | 6 | Duluth Dukes | Pat Neshek |
| 157 | 20 | 7 | New Jersey Patriots | Casey Fossum |
| 158 | 20 | 8 | Nashua Nonames | Ruddy Lugo |
| 159 | 20 | 9 | Santa Clara Leopardos | Matt Guerrier |
| 160 | 20 | 10 | Binghamton Senators | Marlon Anderson |
| 161 | 20 | 11 | Bellingham Pilots | Damian Miller |
| 162 | 20 | 12 | Maui Stingrays | Duaner Sanchez |
| 163 | 20 | 13 | Detroit Wheels | Taylor Tankersley |
| 164 | 20 | 14 | Carolina Sandlappers | Omar Infante |
| 165 | 20 | 15 | Galway Galleons | Adam Lind |
| 166 | 20 | 16 | Texas Lightning | Zach Miner |
| 167 | 20 | 17 | Washington Grays | Chris Coste |
| 168 | 20 | 18 | Bocomo Blues | Horacio Ramirez |
| 169 | 20 | 19 | Nashua Nonames | Mike O'Connor |
| 170 | 20 | 20 | Mystic Sea Horses | Chan Ho Park |
| 171 | 20 | 21 | Kissimmee Cardinals | David Aardsma |
| 172 | 20 | 22 | Hollywood Heat | Kevin Correia |
| 173 | 20 | 23 | Scottsdale Cougars | Braden Looper |
| 174 | 20 | 24 | Dresden Blacks | Elizier Alfonzo |
| 175 | 20 | 25 | Seoul Fighters | Jamey Wright |
| 176 | 20 | 26 | Cambridge Longfellows | Rick Bauer |
| 177 | 21 | 1 | New Orleans Pelicans | Tony Armas |
| 178 | 21 | 2 | Charlotte Knights | Todd Wellemeyer |
| 179 | 21 | 3 | Madiba United | Chris Britton |
| 180 | 21 | 4 | Rosehaven River Dogs | Wes Helms |
| 181 | 21 | 5 | Tampa Bay Pirates | Byung Hung Kim |
| 182 | 21 | 6 | Duluth Dukes | Rob Mackowiak |
| 183 | 21 | 7 | New Jersey Patriots | Ryan Theriot |
| 184 | 21 | 8 | Nashua Nonames | David Dellucci |
| 185 | 21 | 9 | Santa Clara Leopardos | Mike Redmond |
| 186 | 21 | 10 | Binghamton Senators | Jamie Walker |
| 187 | 21 | 11 | Bellingham Pilots | Rod Barajas |
| 188 | 21 | 12 | Maui Stingrays | Wil Ledezma |
| 189 | 21 | 13 | Detroit Wheels | Corey Hart |
| 190 | 21 | 14 | Carolina Sandlappers | Wes Littleton |
| 191 | 21 | 15 | Galway Galleons | Willy Aybar |
| 192 | 21 | 16 | Texas Lightning | Mike Lieberthal |
| 193 | 21 | 17 | Washington Grays | Russell Branyan |
| 194 | 21 | 18 | Bocomo Blues | Damaso Marte |
| 195 | 21 | 19 | Camano Island Wormburners | Brandon Medders |
| 196 | 21 | 20 | Mystic Sea Horses | Hector Luna |
| 197 | 21 | 21 | Kissimmee Cardinals | Brandon Lyon |
| 198 | 21 | 22 | Hollywood Heat | Scott Baker |
| 199 | 21 | 23 | Scottsdale Cougars | Scott Hatteberg |
| 200 | 21 | 24 | Dresden Blacks | Chad Gaudin |
| 201 | 21 | 25 | Seoul Fighters | Greg Norton |
| 202 | 21 | 26 | Cambridge Longfellows | Mark Loretta |
| 203 | 22 | 1 | New Orleans Pelicans | Carlos Villanueva |
| 204 | 22 | 2 | Charlotte Knights | Eric Hinske |
| 205 | 22 | 3 | Madiba United | Luis Vizcaino |
| 206 | 22 | 4 | Rosehaven River Dogs | Todd Coffey |
| 207 | 22 | 5 | Tampa Bay Pirates | Justin Speier |
| 208 | 22 | 6 | Duluth Dukes | Michael Wuertz |
| 209 | 22 | 7 | New Jersey Patriots | Kyle Lohse |
| 210 | 22 | 8 | Nashua Nonames | Josh Hancock |
| 211 | 22 | 9 | Santa Clara Leopardos | Craig Counsell |
| 212 | 22 | 10 | Binghamton Senators | Robb Quinlan |
| 213 | 22 | 11 | Bellingham Pilots | Mackay McBride |
| 214 | 22 | 12 | Maui Stingrays | Chad Paronto |
| 215 | 22 | 13 | Detroit Wheels | Saul Rivera |
| 216 | 22 | 14 | Carolina Sandlappers | Jason Frasor |
| 217 | 22 | 15 | Galway Galleons | John Grabow |
| 218 | 22 | 16 | Texas Lightning | Ronny Cedeno |
| 219 | 22 | 17 | Washington Grays | Jeff Cirillo |
| 220 | 22 | 18 | Bocomo Blues | Jason Kubel |
| 221 | 22 | 19 | Nashua Nonames | Alex Gonzalez |
| 222 | 22 | 20 | Mystic Sea Horses | Elizardo Ramirez |
| 223 | 22 | 21 | Kissimmee Cardinals | Brian Tallet |
| 224 | 22 | 22 | Hollywood Heat | Jose Uribe |
| 225 | 22 | 23 | Scottsdale Cougars | Juan Encarnacion |
| 226 | 22 | 24 | Dresden Blacks | Jonathan Sanchez |
| 227 | 22 | 25 | Seoul Fighters | Mark Redman |
| 228 | 22 | 26 | Cambridge Longfellows | Doug Mientkiewicz |
| 229 | 23 | 1 | New Orleans Pelicans | Brian Sweeney |
| 230 | 23 | 2 | Charlotte Knights | Scott Elarton |
| 231 | 23 | 3 | Bocomo Blues | Josh Kinney |
| 232 | 23 | 4 | Rosehaven River Dogs | Marco Scutaro |
| 233 | 23 | 5 | Tampa Bay Pirates | Roberto Hernandez |
| 234 | 23 | 6 | Duluth Dukes | Robinson Tejeda |
| 235 | 23 | 7 | New Jersey Patriots | Scott Schoeneweiss |
| 236 | 23 | 8 | Nashua Nonames | Corey Koskie |
| 237 | 23 | 9 | Santa Clara Leopardos | Olmedo Saenz |
| 238 | 23 | 10 | Binghamton Senators | Bernie Williams |
| 239 | 23 | 11 | Bellingham Pilots | Russ Springer |
| 240 | 23 | 12 | Maui Stingrays | Rheal Cormier |
| 241 | 23 | 13 | Detroit Wheels | Henry Blanco |
| 242 | 23 | 14 | Carolina Sandlappers | Pablo Ozuna |
| 243 | 23 | 15 | Galway Galleons | Bobby Keilty |
| 244 | 23 | 16 | Texas Lightning | Scott Podsednik |
| 245 | 23 | 17 | Washington Grays | Chris Sampson |
| 246 | 23 | 18 | Bocomo Blues | Elmer Dessens |
| 247 | 23 | 19 | Nashua Nonames | Mike Stanton |
| 248 | 23 | 20 | Mystic Sea Horses | Kirk Saarloos |
| 249 | 23 | 21 | Kissimmee Cardinals | Jeremy Affeldt |
| 250 | 23 | 22 | Hollywood Heat | Fabio Castro |
| 251 | 23 | 23 | Santa Clara Leopardos | Jake Woods |
| 252 | 23 | 24 | Dresden Blacks | Shaun Marcum |
| 253 | 23 | 25 | Seoul Fighters | Jason Michaels |
| 254 | 23 | 26 | Cambridge Longfellows | Cha Seung Baek |
| 255 | 24 | 1 | New Orleans Pelicans | George Sherrill |
| 256 | 24 | 2 | Charlotte Knights | C.J.Wilson |
| 257 | 24 | 3 | Madiba United | Ryan Garko |
| 258 | 24 | 4 | Rosehaven River Dogs | Kevin Gregg |
| 259 | 24 | 5 | Tampa Bay Pirates | Chris Duffy |
| 260 | 24 | 6 | Duluth Dukes | Kaz Matsui |
| 261 | 24 | 7 | New Jersey Patriots | Alex Escobar |
| 262 | 24 | 8 | Nashua Nonames | Tim Salmon |
| 263 | 24 | 9 | Santa Clara Leopardos | Joe Kennedy |
| 264 | 24 | 10 | Binghamton Senators | Dave Borkowski |
| 265 | 24 | 11 | Bellingham Pilots | Phil Nevin |
| 266 | 24 | 12 | Maui Stingrays | Brian Corey |
| 267 | 24 | 13 | Detroit Wheels | Randy Wolf |
| 268 | 24 | 14 | Carolina Sandlappers | Ron Villone |
| 269 | 24 | 15 | Galway Galleons | Craig Wilson |
| 270 | 24 | 16 | Texas Lightning | Matt Smith |
| 271 | 24 | 17 | Washington Grays | Miguel Montero |
| 272 | 24 | 18 | Bocomo Blues | Pablo Torrealba |
| 273 | 24 | 19 | Camano Island Wormburners | Ambiorix Burgos |
| 274 | 24 | 20 | Mystic Sea Horses | Jason Tyner |
| 275 | 24 | 21 | Kissimmee Cardinals | Shin Soo-Choo |
| 276 | 24 | 22 | Hollywood Heat | Ryan Spilborghs |
| 277 | 24 | 23 | Scottsdale Cougars | Darryl Ward |
| 278 | 24 | 24 | Dresden Blacks | Chris Gomez |
| 279 | 24 | 25 | Seoul Fighters | Carlos Silva |
| 280 | 24 | 26 | Cambridge Longfellows | Scott Feldman |
| 281 | 25 | 1 | New Orleans Pelicans | Adam Eaton |
| 282 | 25 | 2 | Charlotte Knights | Alfredo Amezaga |
| 283 | 25 | 3 | Madiba United | Joe Inglett |
| 284 | 25 | 4 | Rosehaven River Dogs | Vance Wilson |
| 285 | 25 | 5 | Tampa Bay Pirates | Sean Casey |
| 286 | 25 | 6 | Duluth Dukes | So Taguchi |
| 287 | 25 | 7 | New Jersey Patriots | Reynel Pinto |
| 288 | 25 | 8 | Nashua Nonames | Javier Valentin |
| 289 | 25 | 9 | Santa Clara Leopardos | Eric Bruntlett |
| 290 | 25 | 10 | Binghamton Senators | Jose Mesa |
| 291 | 25 | 11 | Bellingham Pilots | Mike Rivera |
| 292 | 25 | 12 | Maui Stingrays | Ramon Martinez |
| 293 | 25 | 13 | Detroit Wheels | Jose Capellan |
| 294 | 25 | 14 | Carolina Sandlappers | Ross Gload |
| 295 | 25 | 15 | Galway Galleons | Mike MacDougal |
| 296 | 25 | 16 | Texas Lightning | Eddie Guardado |
| 297 | 25 | 17 | Washington Grays | Charlie Haegar |
| 298 | 25 | 18 | Bocomo Blues | Brian Bannister |
| 299 | 25 | 19 | Camano Island Wormburners | Jose Molina |
| 300 | 25 |