| Round One | Original | Player Picked | Round Six | Original | Player Picked | ||
| 1 | Boca Barons | Mark Prior | 101 | Boca Barons | Carl Everett | ||
| 2 | Texas Hurricanes | Samoan | Eric Hinske | 102 | Samoan Swat Team | George Lombard | |
| 3 | Long Hill Lancers | Austin Kearns |
103 | Long Hill Lancers | Aaron Myette | ||
| 4 | Houston Space Cowboys | Carl Crawford |
104 | Houston Space Cowboys | Jon Rauch | ||
| 5 | Lemont Lounge Lizards | Rodrigo Lopez | 105 | Lemont Lounge Lizards | Rod Barajas | ||
| 6 | Lemont Lounge Lizards | Orland | Oliver Perez | 106 | Orland Jackhammers | Rob Bell | |
| 7 | Minnesota Mashers | Hank Blalock | 107 | Minnesota Mashers | Blaine Neal | ||
| 8 | Hampton Roads Hornets | John Lackey | 108 | Hampton Roads Hornets | Andy Van Hekken | ||
| 9 | Texas Hurricanes | Alcatraz | Victor Martinez | 109 | Alcatraz Pinstripers | John Mabry | |
| 10 | Graylake Cubs | Francisco Rodriguez | 110 | Graylake Cubs | Chad Zerbe | ||
| 11 | Tempe Diablos | Kazuhisa Ishii | 111 | Tempe Diablos | Drew Henson | ||
| 12 | Virginia Beach Seadawg | Sean Burroughs | 112 | Virginia Beach Seadawgs | Tony Alverez | ||
| 13 | Winnipeg Goldeyes | Chris Woodward | 113 | Winnipeg Goldeyes | Jason Middlebrook | ||
| 14 | Texas Hurricanes | Boston | Orlando Hudson |
114 | Boston Bozos | Dennis Tankersley | |
| 15 | Buffalo B.A.D. Boys | Ramon Vazquez |
115 | Buffalo B.A.D. Boys | Brian Meadows | ||
| 16 | Long Hill Lancers | Texas | Jake Peavy |
116 | Texas Hurricanes | Matt Cepicky | |
| 17 | Vancouver Rockhounds | Brandon Phillips |
117 | Vancouver Rockhounds | Wily Mo Pena | ||
| 18 | Northeastern Seawolves | Tom Fiore |
118 | Northeastern Seawolves | A.J. Hinch | ||
| 19 | Puget Sound Orcas | Jason Simontacchi | 119 | Puget Sound Orcas | Jimmy Anderson | ||
| 20 | San Francisco Seals | Mark Ellis | 120 | San Francisco Seals | Zach Day | ||
| Round Two | Round Seven | ||||||
| 21 | Boca Barons | Kris Benson | 121 | Boca Barons | Rey Sanchez | ||
| 22 | Samoan Swat Team | Bobby Hill | 122 | Samoan Swat Team | Julio Santana | ||
| 23 | Long Hill Lancers | Kevin Mench |
123 | Long Hill Lancers | Eric Byrnes | ||
| 24 | Houston Space Cowboys | Brett Myers |
124 | Houston Space Cowboys | Miguel Asencio | ||
| 25 | Lemont Lounge Lizards | Joe Thurston | 125 | Lemont Lounge Lizards | Brian Tallet | ||
| 26 | Orland Jackhammers | Joe Borchard | 126 | Orland Jackhammers | Brandon Puffer | ||
| 27 | Minnesota Mashers | Francisco Cordero | 127 | Winnipeg Goldeyes | Minnesota | Ben Broussard | |
| 28 | Hampton Roads Hornets | Hee Seop Choi | 128 | Hampton Roads Hornets | Mike Bascik | ||
| 29 | Alcatraz Pinstripers | John Patterson | 129 | Alcatraz Pinstripers | Jose Molina | ||
| 30 | Graylake Cubs | Runelvys Hernandez | 130 | Graylake Cubs | Willie Harris | ||
| 31 | Tempe Diablos | Chris Stynes | 131 | Tempe Diablos | Mike Matthews | ||
| 32 | Virginia Beach Seadawgs | Mike Maroth | 132 | Virginia Beach Seadawgs | Shawn Sedlacek | ||
| 33 | Winnipeg Goldeyes | Mike Koplove | 133 | Winnipeg Goldeyes | Aaron Cook | ||
| 34 | Boston Bozos | Rafael Soriano | 134 | Boston Bozos | Kevin Cash | ||
| 35 | Long Hill Lancers | Buffalo | Aaron Harang | 135 | Buffalo B.A.D. Boys | Tony Torcato | |
| 36 | Texas Hurricanes | Marlon Byrd | 136 | Texas Hurricanes | Clay Condrey | ||
| 37 | Vancouver Rockhounds | Cliff Lee | 137 | Vancouver Rockhounds | Vance Wilson | ||
| 38 | Northeastern Seawolves | Chris Hammond | 138 | Northeastern Seawolves | T. J. Tucker | ||
| 39 | Puget Sound Orcas | Quiton McCracken | 139 | Puget Sound Orcas | Jim Brower | ||
| 40 | San Francisco Seals | Frank Castillo | 140 | San Francisco Seals | Tom Prince | ||
| Round Three | Round Eight | ||||||
| 41 | Boca Barons | Travis Hafner | 141 | Boca Barons | Robert Machado | ||
| 42 | Samoan Swat Team | Dave Roberts | 142 | Samoan Swat Team | Ken Huckaby | ||
| 43 | Long Hill Lancers | Mo Vaughn | 143 | Long Hill Lancers | Chad Hermansen | ||
| 44 | Orland Jackhammers | Houston | Kirk Saarloos | 144 | Houston Space Cowboys | Gary Knotts | |
| 45 | Lemont Lounge Lizards | Brandon Larson | 145 | Lemont Lounge Lizards | Jamie Walker | ||
| 46 | Texas Hurricanes | Boston# | Omar Infante | 146 | Orland Jackhammers | Dave Williams | |
| 47 | Winnipeg Goldeyes | Minnesota | Darren Holmes | 147 | Minnesota Mashers | Trey Hodges | |
| 48 | Hampton Roads Hornets | Miguel Olivo | 148 | Hampton Roads Hornets | Andres Torres | ||
| 49 | Texas Hurricanes | Alcatraz | Coco Crisp | 149 | Alcatraz Pinstripers | Lance Carter | |
| 50 | Graylake Cubs | Brian Anderson | 150 | Graylake Cubs | Shane Nance | ||
| 51 | Tempe Diablos | Andy Benes | 151 | Tempe Diablos | Joey Hamilton | ||
| 52 | Virginia Beach Seadawgs | Dewon Brazelton | 152 | Virginia Beach Seadawgs | Todd Greene | ||
| 53 | Winnipeg Goldeyes | Chris Snelling | 153 | Winnipeg Goldeyes | Tim Drew | ||
| 54 | Texas Hurricanes | Boston | Chad Moeller | 154 | Boston Bozos | John Stephens | |
| 55 | Buffalo B.A.D. Boys | Brendan Donnelly | 155 | Buffalo B.A.D. Boys | Jose Leon | ||
| 56 | Samoan Swat Team | Texas% | Jason Durocher | 156 | Texas Hurricanes | Kevin Gryboski | |
| 57 | Vancouver Rockhounds | Michael Restovich | 157 | Vancouver Rockhounds | Pablo Ozuna | ||
| 58 | Northeastern Seawolves | Carlos Silva | 158 | Northeastern Seawolves | Luther Hackman | ||
| 59 | Puget Sound Orcas | Mike Crudale | 159 | Puget Sound Orcas | Jaime Cerda | ||
| 60 | San Francisco Seals | Tom Wilson | 160 | San Francisco Seals | Gregg Zaun | ||
| Round Four | Round Nine | ||||||
| 61 | Boca Barons | Josh Bard | 161 | Boca Barons | Julio Franco | ||
| 62 | Samoan Swat Team | Michael Tejera | 162 | Samoan Swat Team | David Riske | ||
| 63 | Long Hill Lancers | Adam Piatt | 163 | Long Hill Lancers | Sportsman Park | ||
| 64 | Houston Space Cowboys | Lyle Overbay | 164 | Houston Space Cowboys | Abraham O. Nunez | ||
| 65 | Orland Jackhammers | Lemont | Jeremy Affeldt | 165 | Lemont Lounge Lizards | Lenny Harris | |
| 66 | Winnipeg Goldeyes | Orland | Ty Wigginton | 166 | Orland Jackhammers | Dan Smith | |
| 67 | Samoan Swat Team | Minnesota | Jason Lane | 167 | Minnesota Mashers | Ryan Bukvich | |
| 68 | Hampton Roads Hornets | Fernando Tatis | 168 | Hampton Roads Hornets | Alexis Gomez | ||
| 69 | Alcatraz Pinstripers | Mark Hendrickson | 169 | Alcatraz Pinstripers | Brian Moehler | ||
| 70 | Graylake Cubs | Ramon Santiago | 170 | Graylake Cubs | Gookie Dawkins | ||
| 71 | Tempe Diablos | Willie Bloomquist | 171 | Tempe Diablos | |||
| 72 | Virginia Beach Seadawgs | Freddy Sanchez | 172 | Virginia Beach Seadawgs | Francis Beltran | ||
| 73 | Winnipeg Goldeyes | Brandon Villafuerte | 173 | Winnipeg Goldeyes | Jason Davis | ||
| 74 | Texas Hurricanes | Boston | Endy Chavez | 174 | Boston Bozos | Chone Figgins | |
| 75 | Buffalo B.A.D. Boys | Gene Kingsale | 175 | Buffalo B.A.D. Boys | Kevin Young | ||
| 76 | Texas Hurricanes | Peter Munro | 176 | Texas Hurricanes | Kelly Wunsch | ||
| 77 | Vancouver Rockhounds | Colby Lewis | 177 | Vancouver Rockhounds | Eduardo Perez | ||
| 78 | Northeastern Seawolves | John McDonald | 178 | Northeastern Seawolves | Jason Conti | ||
| 79 | Puget Sound Orcas | Miguel Cairo | 179 | Puget Sound Orcas | Kerry Robinson | ||
| 80 | San Francisco Seals | Adam Hyzdu | 180 | San Francisco Seals | Danny Kolb | ||
| Round Five | Round Ten | ||||||
| 81 | Boca Barons | Jeromy Burnitz | 181 | Boca Barons | Edison Field | ||
| 82 | Samoan Swat Team | Velerio De Los Santos | 182 | Samoan Swat Team | Steve Cox | ||
| 83 | Long Hill Lancers | Jason Grabowski | 183 | Long Hill Lancers | roster full | ||
| 84 | Houston Space Cowboys | Morgan Ensberg | 184 | Houston Space Cowboys | John Valentin | ||
| 85 | Lemont Lounge Lizards | Mark Quin | 185 | Lemont Lounge Lizards | Tomas Perez | ||
| 86 | Orland Jackhammers | Antonio Osuna | 186 | Orland Jackhammers | Todd Jones | ||
| 87 | Minnesota Mashers | Duaner Sanchez | 187 | Minnesota Mashers | J J Davis | ||
| 88 | Hampton Roads Hornets | Jayson Werth | 188 | Hampton Roads Hornets | Jason Romano | ||
| 89 | Alcatraz Pinstripers | Matt Franco | 189 | Alcatraz Pinstripers | Scott Mullen | ||
| 90 | Graylake Cubs | Sandy Alomar | 190 | Graylake Cubs | Josh Paul | ||
| 91 | Tempe Diablos | Matt Mantei | 191 | Tempe Diablos | Ricky Henderson | ||
| 92 | Virginia Beach Seadawgs | Brad Lidge | 192 | Virginia Beach Seadawgs | Jason Hart | ||
| 93 | Winnipeg Goldeyes | Ryan Ludwick | 193 | Boston Bozos | Winnipeg | Jason Phillips | |
| 94 | Boston Bozos | Ricardo Rodriguez | 194 | Boston Bozos | Nate Cornejo | ||
| 95 | Buffalo B.A.D. Boys | Jamey Carroll | 195 | Buffalo B.A.D. Boys | Jason Michaels | ||
| 96 | Samoan Swat Team | Texas | Eric Munson | 196 | Texas Hurricanes | roster full | |
| 97 | Vancouver Rockhounds | Franklyn German | 197 | Vancouver Rockhounds | Rolando Arrojo | ||
| 98 | Northeastern Seawolves | Joe Roa | 198 | Northeastern Seawolves | Orlando Merced | ||
| 99 | Orland Jackhammers | Boston * | Guillermo Mota | 199 | Puget Sound Orcas | Mike Fyhrie | |
| 100 | San Francisco Seals | Pete Walker | 200 | San Francisco Seals | Greg Myers | ||
| *-pick 99 Kingston, #-pick 46 Orland, %-pick 56 Texas | 201 | Boca Barons | Shane Spencer | ||||
| 202 | Samoan Swat Team | Tom Lampkin | |||||
| 203 | Lemont Lounge Lizards | Wendall Magee | |||||
| 204 | Minnesota Mashers | Bobby Estallela | |||||
| 205 | Hampton Road Hornets | Scott Cassidy | |||||
| 206 | Graylake Cubs | Travis Harper | |||||
| 207 | Tempe Diablos | Jorge Sosa | |||||
| 208 | Boston Bozos | Estaban German | |||||
| 209 | Minnesota Mashers | Pat Strange | |||||
| 210 | Boston Bozos | Chin-Feng Chen | |||||
| 211 | Buffalo B.A.D. Boys | Charles Gibson | |||||
| 212 | Vancouver Rockhounds | Frank Menechino | |||||
| 213 | Puget Sound Orcas | Brian Bowles | |||||
| 214 | Hampton Road Hornets | Mike Callaway | |||||
| 215 | San Francisco Seals | Carlos Almanzar | |||||
| 216 | Boston Bozos | Chad Kreuter | |||||
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