| Round 1 | |||
| Team | Player | ||
| 1 | Fort Brags | Ryan J. Braun (3B MIL) | |
| 2 | Pompano Sugar Kings | Carlos Beltran (OF NYM) | |
| 3 | New York Knights | Tim Lincecum (P SF) | |
| 4 | Rock River Catfish | Aaron Harang (P CIN) | |
| 5 | Dyersville Spirits | Yovani Gallardo (P MIL) | |
| 6 | Kentucky Head Hunters | Hunter Pence (OF HOU) | |
| 7 | Kentucky Head Hunters | Justin Upton (OF ARI) | |
| 8 | Mid-Atlantic Diamond Angels | Micah Owings (P ARI) | |
| 9 | North Coast Clippers | Tim Hudson (P ATL) | |
| 10 | Dyersville Spirits | Derek Lowe (P LA) | |
| 11 | East Saint Flyers | Josh Hamilton (OF TEX) | |
| 12 | Fort Brags | Jason Isringhausen (P STL) | |
| 13 | Ontario River Kings | Yunel Escobar (SS ATL) | |
| 14 | Fort Liquordale Flounders | Doug Davis (P ARI) | |
| 15 | Kentucky Head Hunters | Andy LaRoche (3B LA) | |
| 16 | Tampico Stogies | Homer Bailey (P CIN) | |
| Round 2 | |||
| 17 | South Florida Chupacabras | Peter Moylan (P ATL) | |
| 18 | Pompano Sugar Kings | Felix Pie (OF CHC) | |
| 19 | Mid-Atlantic Diamond Angels | Derrick Turnbow (P MIL) | |
| 20 | Rock River Catfish | Franklin Morales (P COL) | |
| 21 | Indy Colts | Joey Votto (1B CIN) | |
| 22 | Indy Colts | Pedro Martinez (P NYM) | |
| 23 | New York Knights | Mark Reynolds (3B ARI) | |
| 24 | Mid-Atlantic Diamond Angels | Randy Winn (OF SF) | |
| 25 | North Coast Clippers | Carlos Delgado (1B NYM) | |
| 26 | Dyersville Spirits | Jayson Werth (OF PHI) | |
| 27 | East Saint Flyers | Matt Herges (P COL) | |
| 28 | Tampico Stogies | J.R. Towles (C HOU) | |
| 29 | Indy Colts | Kyle Kendrick (P PHI) | |
| 30 | Pompano Sugar Kings | Jesus Flores (C WAS) | |
| 31 | Kentucky Head Hunters | Chase Headley (3B SD) | |
| 32 | Fort Brags | Jared Burton (P CIN) | |
| Round 3 | |||
| 33 | Dyersville Spirits | Troy Percival (P TB) | |
| 34 | Pompano Sugar Kings | Chin-lung Hu (SS LA) | |
| 35 | Kentucky Head Hunters | Steve Pearce (OF PIT) | |
| 36 | Rock River Catfish | Manny Parra (P MIL) | |
| 37 | Ontario River Kings | Rick Ankiel (OF STL) | |
| 38 | Indy Colts | Matt Chico (P WAS) | |
| 39 | Fort Brags | Justin Miller (P FLA) | |
| 40 | Mid-Atlantic Diamond Angels | Mike Cameron (OF MIL) | |
| 41 | North Coast Clippers | Tony Abreu (3B LA) | |
| 42 | Kentucky Head Hunters | Ross Detwiler (P WAS) | |
| 43 | East Saint Flyers | Mike Lamb (3B MIN) | |
| 44 | Tampico Stogies | Zach Duke (P PIT) | |
| 45 | Fort Brags | Jorge Sosa (P NYM) | |
| 46 | Pompano Sugar Kings | Carlos Gomez (OF MIN) | |
| 47 | Fort Brags | Omar Vizquel (SS SF) | |
| 48 | Fort Liquordale Flounders | Rick VandenHurk (P FLA) | |
| Round 4 | |||
| 49 | 49 | South Florida Chupacabras | Scott Linebrink (P CHW) |
| 50 | 50 | Tampico Stogies | Mark Prior (P SD) |
| 51 | 51 | New York Knights | Jo-Jo Reyes (P ATL) |
| 52 | Rock River Catfish | Manny Acosta (P ATL) | |
| 53 | Atlanta Argonauts | Tim Redding (P WAS) | |
| 54 | Indy Colts | Jack Taschner (P SF) | |
| 55 | Kentucky Head Hunters | Troy Patton (P BAL) | |
| 56 | Mid-Atlantic Diamond Angels | Joe Thatcher (P SD) | |
| 57 | North Coast Clippers | D'Angelo Jimenez (2B STL) | |
| 58 | Tampico Stogies | Mark Mulder (P STL) | |
| 59 | New York Knights | Felipe Paulino (P HOU) | |
| 60 | Tampico Stogies | Jason Jennings (P TEX) | |
| 61 | Ontario River Kings | Damion Easley (2B NYM) | |
| 62 | Fort Liquordale Flounders | Ryan Ludwick (OF STL) | |
| 63 | South Florida Chupacabras | Josh Phelps (1B STL) | |
| 64 | Atlanta Argonauts | Chin-Hui Tsao (P KC) | |
| Round 5 | |||
| 65 | Fort Liquordale Flounders | Matt Lindstrom (P FLA) | |
| 66 | Pompano Sugar Kings | Guillermo Mota (P MIL) | |
| 67 | Tampico Stogies | Brandon Jones (OF ATL) | |
| 68 | Rock River Catfish | Kevin Hart (P CHC) | |
| 69 | Atlanta Argonauts | Jon Coutlangus (P CIN) | |
| 70 | North Coast Clippers | Lee Gardner (P FLA) | |
| 71 | Kentucky Head Hunters | Jonathan Meloan (P LA) | |
| 72 | Mid-Atlantic Diamond Angels | Alfredo Amezaga (OF FLA) | |
| 73 | North Coast Clippers | Doug Slaten (P ARI) | |
| 74 | Toledo Mud Hens | Norris Hopper (OF CIN) | |
| 75 | East Saint Flyers | Kip Wells (P COL) | |
| 76 | Tampico Stogies | Nate Schierholtz (OF SF) | |
| 77 | Dyersville Spirits | Brett Tomko (P KC) | |
| 78 | Fort Liquordale Flounders | Josh Johnson (P FLA) | |
| 79 | Kentucky Head Hunters | Juan Gutierrez (P ARI) | |
| 80 | Mid-Atlantic Diamond Angels | Dave Roberts (OF SF) | |
| Round 6 | |||
| 81 | Kentucky Head Hunters | Joey Devine (P OAK) | |
| 82 | Pompano Sugar Kings | John Lannan (P WAS) | |
| 83 | Fort Brags | Jonathan Albaladejo (P NYY) | |
| 84 | Kentucky Head Hunters | Joe Smith (P NYM) | |
| 85 | Mid-Atlantic Diamond Angels | Ruben Gotay (2B NYM) | |
| 86 | Indy Colts | Rajai Davis (OF SF) | |
| 87 | Kentucky Head Hunters | J.A. Happ (P PHI) | |
| 88 | Mid-Atlantic Diamond Angels | Miguel Olivo (C KC) | |
| 89 | North Coast Clippers | Fred Lewis (OF SF) | |
| 90 | Toledo Mud Hens | David Eckstein (SS TOR) | |
| 91 | East Saint Flyers | Rudy Seanez (P LA) | |
| 92 | Tampico Stogies | Nyjer Morgan (OF PIT) | |
| 93 | Ontario River Kings | Mike Gonzalez (P ATL) | |
| 94 | Tampico Stogies | Tony Clark (1B SD) | |
| 95 | Toledo Mud Hens | Buddy Carlyle (P ATL) | |
| 96 | Dyersville Spirits | Brendan Ryan (SS STL) | |
| Round 7 | |||
| 97 | Kentucky Head Hunters | Jeff Suppan (P MIL) | |
| 98 | Ontario River Kings | Joe Dillon (OF MIL) | |
| 99 | Dyersville Spirits | Javier Valentin (C CIN) | |
| 100 | Indy Colts | Kevin Cameron (P SD) | |
| 101 | Indy Colts | Aaron Miles (2B STL) | |
| 102 | Indy Colts | Dennis Sarfate (P BAL) | |
| 103 | Kentucky Head Hunters | Sean Gallagher (P CHC) | |
| 104 | Mid-Atlantic Diamond Angels | Chris Duffy (OF PIT) | |
| 105 | North Coast Clippers | Mike Fontenot (2B CHC) | |
| 106 | Toledo Mud Hens | Guillermo Rodriguez (C SF) | |
| 107 | East Saint Flyers | Brad Salmon (P CIN) | |
| 108 | Tampico Stogies | Juan Morillo (P COL) | |
| 109 | Tampico Stogies | Mike Bacsik (P WAS) | |
| 110 | Tampico Stogies | Cristian Guzman (SS WAS) | |
| 111 | Atlanta Argonauts | Pete Laforest (C PHI) | |
| 112 | Fort Brags | Brandon Duckworth (P KC) | |
| Round 8 | |||
| South Florida Chupacabras | Brandon Backe (P HOU) | ||
| Fort Liquordale Flounders | Joe Bisenius (P PHI) | ||
| Toledo Mud Hens | Daniel Barone (P FLA) | ||
| 116 | Rock River Catfish | Dave Borkowski (P HOU) | |
| 117 | Kentucky Head Hunters | Justin Maxwell (OF WAS) | |
| 118 | New York Knights | Skip Schumaker (OF STL) | |
| 119 | Fort Brags | Mark S. McLemore (P HOU) | |
| 120 | Toledo Mud Hens | Nomar Garciaparra (1B LA) | |
| 121 | North Coast Clippers | Robby Hammock (C ARI) | |
| 122 | Ontario River Kings | Jose Ascanio (P CHC) | |
| 123 | East Saint Flyers | Marcus Giles (2B COL) | |
| 124 | Fort Brags | Emilio Bonifacio (2B ARI) | |
| 125 | Ontario River Kings | Tom Shearn (P CIN) | |
| 126 | New York Knights | Brandon Medders (P ARI) | |
| 127 | Dyersville Spirits | Endy Chavez (OF NYM) | |
| 128 | Ontario River Kings | Tyler Walker (P SF) | |
| Round 9 | |||
| 129 | South Florida Chupacabras | Duaner Sanchez (P NYM) | |
| 130 | Pompano Sugar Kings | J.D. Durbin (P PHI) | |
| 131 | Kentucky Head Hunters | Henry Blanco (C CHC) | |
| 132 | Rock River Catfish | Juan Encarnacion (OF STL) | |
| 133 | Fort Brags | Brad Thompson (P STL) | |
| 134 | Indy Colts | Cory Sullivan (OF COL) | |
| 135 | Fort Brags | Joe Koshansky (1B COL) | |
| 136 | Mid-Atlantic Diamond Angels | Eric Milton (P CIN) | |
| 137 | Indy Colts | Joel Hanrahan (P WAS) | |
| 138 | East Saint Flyers | Russell Branyan (3B STL) | |
| 139 | East Saint Flyers | Victor Santos (P SF) | |
| 140 | Fort Brags | Eric Patterson (OF CHC) | |
| 141 | Ontario River Kings | Ray Durham (2B SF) | |
| 142 | Dyersville Spirits | Cesar Izturis (SS STL) | |
| 143 | Fort Brags | Kory Casto (OF WAS) | |
| 144 | Fort Brags | Eliezer Alfonzo (C SF) | |
| Round 10 | |||
| 145 | Fort Brags | Mike Zagurski (P PHI) | |
| 146 | Pompano Sugar Kings | Jeff Bennett (P ATL) | |
| 147 | North Coast Clippers | Romulo Sanchez (P PIT) | |
| 148 | East Saint Flyers | Marcus McBeth (P CIN) | |
| 149 | Ontario River Kings | Elmer Dessens (P PIT) | |
| 150 | Indy Colts | Bryan Bullington (P PIT) | |
| 151 | Kentucky Head Hunters | No Pick! (skipped during draft) | |
| 152 | Fort Liquordale Flounders | Augie Ojeda (2B ARI) | |
| 153 | Indy Colts | Carlos Martinez (P FLA) | |
| 154 | Mid-Atlantic Diamond Angels | Mitch Stetter (P MIL) | |
| 155 | East Saint Flyers | Koyie Hill (C CHC) | |
| 156 | Fort Liquordale Flounders | John Van Benschoten (P PIT) | |
| 157 | Ontario River Kings | Josh Anderson (OF ATL) | |
| 158 | Fort Liquordale Flounders | Sam Fuld (OF CHC) | |
| 159 | Ontario River Kings | Jeff Salazar (OF ARI) | |
| 160 | Tampico Stogies | No Pick! (skipped during draft) | |
| Round 11 | |||
| 161 | South Florida Chupacabras | No Pick! (skipped during draft) | |
| 162 | Pompano Sugar Kings | No Pick! (skipped during draft) | |
| 163 | East Saint Flyers | Jose Mesa (P PHI) | |
| 164 | North Coast Clippers | No Pick! (skipped during draft) | |
| 165 | Atlanta Argonauts | Ryan Wagner (P WAS) | |
| 166 | Indy Colts | No Pick! (skipped during draft) | |
| 167 | Kentucky Head Hunters | No Pick! (skipped during draft) | |
| 168 | Mid-Atlantic Diamond Angels | Russ Ortiz (P SF) | |
| 169 | North Coast Clippers | No Pick! (skipped during draft) | |
| 170 | Indy Colts | No Pick! (skipped during draft) | |
| 171 | East Saint Flyers | Jack Cassel (P HOU) | |
| 172 | Indy Colts | Kelly Stinnett (C NYM) | |
| 173 | Indy Colts | Franqueline Osorai (P PIT) | |