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 |