| 2006 Draft Results | ||||
| Round 1 | ||||
| 1 | Kentucky Head Hunters | Nick Johnson (1B WAS) | ||
| 2 | Rock River Catfish | Zach Duke (P PIT) | ||
| 3 | Connecticut Chupacabras | Jeff Francoeur (OF ATL) | ||
| 4 | Fort Liquordale Flounders | Jeremy Hermida (OF FLA) | ||
| 5 | Connecticut Chupacabras | Ryan Zimmerman (3B WAS) | ||
| 6 | Tampico Shockers | Felipe Lopez (SS CIN) | ||
| 7 | Rutherford Owls | Matt Cain (P SF) | ||
| 8 | Milwaukee Beers | Joey N. Devine (P ATL) | ||
| 9 | Fort Liquordale Flounders | Paul Maholm (P PIT) | ||
| 10 | East Saint Flyers | Hector Carrasco (P ANA) | ||
| 11 | North Coast Clippers | Brian McCann (C ATL) | ||
| 12 | Kentucky Head Hunters | Conor Jackson (1B ARI) | ||
| 13 | Kentucky Head Hunters | Edwin Encarnacion (3B CIN) | ||
| 14 | Fort Brags | Matt Murton (OF CHC) | ||
| 15 | Pompano Sugar Kings | Juan Uribe (SS CHW) | ||
| 16 | Toledo Mud Hens | Mike Jacobs (1B FLA) | ||
| Round 2 | ||||
| 17 | Indianapolis Indians | Will Ohman (P CHC) | ||
| 18 | Rock River Catfish | Scott Olsen (P FLA) | ||
| 19 | Connecticut Chupacabras | Dioner Navarro (C LA) | ||
| 20 | Fort Liquordale Flounders | Jason M. Vargas (P FLA) | ||
| 21 | Connecticut Chupacabras | Juan Encarnacion (OF STL) | ||
| 22 | Tampico Shockers | Kenny Lofton (OF LA) | ||
| 23 | Rock River Catfish | Cory Lidle (P PHI) | ||
| 24 | Milwaukee Beers | Pete Walker (P TOR) | ||
| 25 | Fort Liquordale Flounders | Ryan Doumit (C PIT) | ||
| 26 | East Saint Flyers | Robinson Tejeda (P PHI) | ||
| 27 | Pompano Sugar Kings | Ryan Shealy (1B COL) | ||
| 28 | Dyersville Spirits | Wandy Rodriguez (P HOU) | ||
| 29 | Kentucky Head Hunters | Cory Sullivan (OF COL) | ||
| 30 | Fort Brags | Juan Padilla (P NYM) | ||
| 31 | Pompano Sugar Kings | Corey Patterson (OF BAL) | ||
| 32 | Dyersville Spirits | Gary Majewski (P WAS) | ||
| Round 3 | ||||
| 33 | Indianapolis Indians | Brad Ausmus (C HOU) | ||
| 34 | Rock River Catfish | Corey C. Hart (OF MIL) | ||
| 35 | Vandelay Industries | Jeff Conine (OF BAL) | ||
| 36 | Fort Liquordale Flounders | Chris Duffy (OF PIT) | ||
| 37 | Kentucky Head Hunters | Freddy Sanchez (3B PIT) | ||
| 38 | Tampico Shockers | Anthony Reyes (P STL) | ||
| 39 | Dyersville Spirits | Ronny Cedeno (SS CHC) | ||
| 40 | Milwaukee Beers | John Foster (P ATL) | ||
| 41 | Indianapolis Indians | Clay Hensley (P SD) | ||
| 42 | East Saint Flyers | Brad Thompson (P STL) | ||
| 43 | North Coast Clippers | Brandon Medders (P ARI) | ||
| 44 | Dyersville Spirits | Marcos Carvajal (P SEA) | ||
| 45 | Milwaukee Beers | Blaine Boyer (P ATL) | ||
| 46 | Fort Brags | Brian Shackelford (P CIN) | ||
| 47 | Tampico Shockers | Jack Taschner (P SF) | ||
| 48 | Connecticut Chupacabras | Edwin Jackson (P TB) | ||
| Round 4 | ||||
| 49 | Connecticut Chupacabras | Jonathan R. Broxton (P LA) | ||
| 50 | Rock River Catfish | Sean Burroughs (3B TB) | ||
| 51 | Toledo Mud Hens | Brad Halsey (P ARI) | ||
| 52 | Fort Liquordale Flounders | Kyle Davies (P ATL) | ||
| 53 | Connecticut Chupacabras | Tom S. Gorzelanny (P PIT) | ||
| 54 | Dyersville Spirits | Antonio Perez (3B OAK) | ||
| 55 | North Coast Clippers | Eduardo Perez (1B CLE) | ||
| 56 | Milwaukee Beers | John Rodriguez (OF STL) | ||
| 57 | Fort Liquordale Flounders | Josh Johnson (P FLA) | ||
| 58 | East Saint Flyers | Russ Springer (P HOU) | ||
| 59 | Pompano Sugar Kings | Brian Lawrence (P WAS) | ||
| 60 | Fort Brags | Kelly Johnson (OF ATL) | ||
| 61 | Kentucky Head Hunters | D.J. Houlton (P LA) | ||
| 62 | Fort Brags | David Cortes (P COL) | ||
| 63 | Tampico Shockers | Anthony Lerew (P ATL) | ||
| 64 | Pompano Sugar Kings | Chris Reitsma (P ATL) | ||
| Round 5 | ||||
| 65 | Indianapolis Indians | Aaron Small (P NYY) | ||
| 66 | Rock River Catfish | Steve Trachsel (P NYM) | ||
| 67 | Dyersville Spirits | Brian Moehler (P FLA) | ||
| 68 | Dyersville Spirits | Orlando Palmeiro (OF HOU) | ||
| 69 | Kentucky Head Hunters | Julio Santana (P PHI) | ||
| 70 | North Coast Clippers | Lance Niekro (1B SF) | ||
| 71 | Vandelay Industries | Pete Orr (2B ATL) | ||
| 72 | Milwaukee Beers | Brandon Watson (OF WAS) | ||
| 73 | Indianapolis Indians | Lenny Harris (3B FLA) | ||
| 74 | East Saint Flyers | Lance Cormier (P ATL) | ||
| 75 | Pompano Sugar Kings | Matt Belisle (P CIN) | ||
| 76 | Dyersville Spirits | Dustin Nippert (P ARI) | ||
| 77 | Dyersville Spirits | Rich Hill (P CHC) | ||
| 78 | Fort Liquordale Flounders | Chris Aguila (OF FLA) | ||
| 79 | Dyersville Spirits | Ezequiel Astacio (P HOU) | ||
| 80 | East Saint Flyers | Oscar Robles (SS LA) | ||
| Round 6 | ||||
| 81 | Pompano Sugar Kings | Tim Stauffer (P SD) | ||
| 82 | Rock River Catfish | Kelly Stinnett (C NYY) | ||
| 83 | New York Knights | Rick Helling (P MIL) | ||
| 84 | Indianapolis Indians | Eric Milton (P CIN) | ||
| 85 | Fort Liquordale Flounders | Josh Fogg (P COL) | ||
| 86 | Tampico Shockers | Macay McBride (P ATL) | ||
| 87 | Rutherford Owls | Vinny Castilla (3B SD) | ||
| 88 | Milwaukee Beers | Jeremy Accardo (P SF) | ||
| 89 | Indianapolis Indians | Mike Burns (P CIN) | ||
| 90 | East Saint Flyers | Randy Keisler (P OAK) | ||
| 91 | Pompano Sugar Kings | Scott Munter (P SF) | ||
| 92 | Fort Brags | Ben Johnson (OF SD) | ||
| 93 | Vandelay Industries | Tony Womack (2B CIN) | ||
| 94 | Fort Brags | Steve Schmoll (P NYM) | ||
| 95 | North Coast Clippers | Damian Jackson (2B WAS) | ||
| 96 | Pompano Sugar Kings | Franklin Gutierrez (OF CLE) | ||
| Round 7 | ||||
| 97 | Rock River Catfish | Dan Kolb (P MIL) | ||
| 98 | Fort Brags | Nelson R. Cruz (OF MIL) | ||
| 99 | Vandelay Industries | Willy Aybar (3B LA) | ||
| 100 | Connecticut Chupacabras | Anderson Hernandez (2B NYM) | ||
| 101 | Tampico Shockers | Brian Meadows (P LA) | ||
| 102 | Dyersville Spirits | Mark DeRosa (OF TEX) | ||
| 103 | Milwaukee Beers | Chuck H. James (P ATL) | ||
| 104 | Dyersville Spirits | Ramon Ortiz (P WAS) | ||
| 105 | Toledo Mud Hens | Jason J. Ellison (OF SF) | ||
| 106 | Pompano Sugar Kings | Edgar G. Gonzalez (P ARI) | ||
| 107 | Dyersville Spirits | Marlon Byrd (OF WAS) | ||
| 108 | Vandelay Industries | Kane Davis (P MIL) | ||
| 109 | Fort Brags | Sean Burnett (P PIT) | ||
| 110 | North Coast Clippers | Nate McLouth (OF PIT) | ||
| 111 | Fort Liquordale Flounders | Brad Eldred (1B PIT) | ||
| 112 | Rutherford Owls | Eddy Garabito (2B BAL) | ||
| Round 8 | ||||
| 113 | Dyersville Spirits | Franquelis Osoria (P LA) | ||
| 114 | Connecticut Chupacabras | Adam Wainwright (P STL) | ||
| 115 | Tampico Shockers | Chris Resop (P FLA) | ||
| 116 | Milwaukee Beers | Todd Coffey (P CIN) | ||
| 117 | Indianapolis Indians | Chris Denorfia (OF CIN) | ||
| 118 | East Saint Flyers | Ryan Wagner (P CIN) | ||
| 119 | Pompano Sugar Kings | Justin Knoedler (C SF) | ||
| 120 | Rutherford Owls | Steve Finley (OF SF) | ||
| 121 | Kentucky Head Hunters | Darrell Rasner (P NYY) | ||
| 122 | Toledo Mud Hens | Royce Ring (P NYM) | ||
| 123 | North Coast Clippers | Omar Quintanilla (SS COL) | ||
| 124 | New York Knights | Juan Cruz (P OAK) | ||
| 125 | North Coast Clippers | Shane Victorino (OF PHI) | ||
| 126 | Fort Brags | Jeff Baker (3B COL) | ||
| 127 | Connecticut Chupacabras | Koyie Hill (C ARI) | ||
| 128 | Tampico Shockers | Matt D. Capps (P PIT) | ||
| Round 9 | ||||
| 129 | Milwaukee Beers | No Pick! (skipped during draft) | ||
| 130 | Indianapolis Indians | Luke Scott (OF HOU) | ||
| 131 | East Saint Flyers | David Ross (C SD) | ||
| 132 | Kentucky Head Hunters | Dana Eveland (P MIL) | ||
| 133 | New York Knights | Damon Hollins (OF TB) | ||
| 134 | Kentucky Head Hunters | Yorman Bazardo (P SEA) | ||
| 135 | Toledo Mud Hens | No Pick! (skipped during draft) | ||
| 136 | North Coast Clippers | Paul Wilson (P CIN) | ||
| 137 | Vandelay Industries | Miguel Ojeda (C COL) | ||
| 138 | Rock River Catfish | No Pick! (skipped during draft) | ||
| 139 | Kentucky Head Hunters | Elizardo Ramirez (P CIN) | ||
| 140 | Kentucky Head Hunters | Adam Melhuse (C OAK) | ||
| 141 | Tampico Shockers | No Pick! (skipped during draft) | ||
| 142 | Milwaukee Beers | No Pick! (skipped during draft) | ||
| 143 | Indianapolis Indians | Jermaine Van Buren (P BOS) | ||
| 144 | Kentucky Head Hunters | No Pick! (skipped during draft) | ||
| Round 10 | ||||
| 145 | New York Knights | Todd Wellemeyer (P CHC) | ||
| 146 | Vandelay Industries | No Pick! (skipped during draft) | ||
| 147 | Rock River Catfish | No Pick! (skipped during draft) | ||
| 148 | Connecticut Chupacabras | No Pick! (skipped during draft) | ||
| 149 | Tampico Shockers | No Pick! (skipped during draft) | ||
| 150 | Indianapolis Indians | William Bergolla (2B CIN) | ||
| 151 | Kentucky Head Hunters | No Pick! (skipped during draft) | ||
| 152 | Vandelay Industries | No Pick! (skipped during draft) | ||
| 153 | Connecticut Chupacabras | No Pick! (skipped during draft) | ||
| 154 | Indianapolis Indians | No Pick! (skipped during draft) | ||
| 155 | Toledo Mud Hens | No Pick! (skipped during draft) | ||
| 156 | Fort Brags | No Pick! (skipped during draft) | ||
| 157 | Connecticut Chupacabras | No Pick! (skipped during draft) | ||
| 158 | Indianapolis Indians | No Pick! (skipped during draft) | ||
| 159 | Fort Brags | No Pick! (skipped during draft) | ||
| 160 | New York Knights | Cal Eldred (P STL) | ||