| Roger (1) | Midwest (2) | Madeleine (3) | Philly (4) | Bethesda (5) | Allegheny (6) | Antelope (7) | Spokane (8) | |||
| Drafted Players | 1 | Elmer Dessens | Brandon Phillips | Kaz Matsui | Luis Matos | Dave Roberts | Jeff Mathis | Keith Ginter | Jeremy Affeldt | |
| 2 | Eli Marrero | Elizardo Ramirez | Jeff Cirillo | Scott Hatteberg | Jason Smith | Runelvys Hernandez | James Baldwin | Shawn Camp | ||
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| 7 | ||||||||||
| Pullbacks | 1 | Brendan Harris | Brad Hennessey | PASS | Maicer Izturis | PASS | Hector Luna | PASS | Jamey Wright | |
| 2 | Larry Bigbie | PASS | Terry Tiffee | PASS | Alex Gonzalez | PASS | Jose Macias | |||
| 3 | Ruben Gotay | PASS | John Mabry | PASS | Brandon League | PASS | Mike Stanton | |||
| 4 | PASS | John Olerud | PASS | PASS | ||||||
| 5 | PASS | PASS | PASS | |||||||
| 6 | PASS | PASS | PASS | |||||||
| Unprotected (Draft Eligible) |
1 | Alomar Jr, Sandy | Adkins, Jon | Borkowski, Dave | Alvarez, Wilson | Chen, Ching-Feng | Bautista, Jose | Fordyce, Brook (IR) | Borders, Pat | |
| 2 | Bennett, Jeff (IR) | Ginter, Matt | Choate, Randy | Batista, Tony (IR) | De Los Santos, Valerio | Garcia, Jairo | Gonzalez, Jeremi | Duckworth, Brandon | ||
| 3 | Colome, Jesus | Hendrickson, Ben (IR) | Dohmann, Scott | Glover, Gary | Hummel, Tim (IR) | German, Esteban | Graman, Alex | Hernandez, Carlos (IR) | ||
| 4 | Glanville, Doug (IR) | Phelps, Josh | Jackson, Mike (IR) | Menechino, Frank | Nunez, Abraham (IR) | Grabow, John | Laker, Tim | Treanor, Matt | ||
| 5 | Mordecai, Mike | Quantrill, Paul | Leicester, Jon | Offerman, Jose | Hairston, Scott | Leskanic, Curt (IR) | Tucker, Michael | |||
| 6 | Redding, Tim | Quintero, Humberto | Leone, Justin (IR) | Powell, Jay | Pellow, Kit (IR) | Nomo, Hideo | ||||
| 7 | Zeile, Todd (IR) | Martin, Tom | Riley, Matt | Remlinger, Mike | ||||||
| 8 | Martinez, Edgar (IR) | Segui, David (IR) | Serrano, Jimmy (IR) | |||||||
| 9 | Munson, Eric | Valentin, Jose | Tsao, Chin-Hui | |||||||
| 10 | Rakers, Aaron | Villafuerte, Brandon (IR) | Wilson, Dan | |||||||
| 11 | Tucker, TJ | |||||||||
| 12 | ||||||||||
| Galaxy (9) | Georgia (10) | Bremerton (11) | High Plains (12) | Durham (13) | Callaway (14) | Chandler (15) | Richmond (16) | |||
| Drafted Players | 1 | Cole Hamels (UNC) | Sean Burroughs | Brian Lawrence | Gerald Laird | Joe Kennedy | Marco Scutaro | Chad Moeller | Juan Dominguez | |
| 2 | Damon Hollins | Todd Pratt | Ramon Ortiz | Scott Spiezio | Alex Sanchez | Tomas Perez | Alex Cora | Raul Chavez | ||
| 3 | ||||||||||
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| 7 | ||||||||||
| Pullbacks | 1 | Justin Germano (IR) | Dan Miceli | Gary Bennett | PASS | PASS | Luis Rivas | Steve Kline | Gabe Gross | |
| 2 | Joe Borowski | Jose Mesa | PASS | SKIPPED | Junior Spivey | Octavio Dotel | ||||
| 3 | SKIPPED | PASS | PASS | |||||||
| 4 | PASS | PASS | ||||||||
| 5 | PASS | PASS | ||||||||
| 6 | PASS | PASS | ||||||||
| Unprotected (Draft Eligible) |
1 | Baek, Cha-Seung (IR) | Amezaga, Alfredo | Blackley, Travis (IR) | Acevedo, Jose | Atchison, Scott | Guiel, Aaron | Bernero, Adam | Anderson, Brian | |
| 2 | Bagwell, Jeff | Baerga, Carlos (IR) | Dobbs, Gary | Berg, Dave (IR) | Christiansen, Jason | Koch, Bily | Carter, Lance | Bartosh, Cliff | ||
| 3 | Clark, Howie (IR) | Burba, Dave | Garcia, Jesse | Johnson, Mark (IR) | Field, Nate | Mantei, Matt | Cormier, Rheal | Grissom, Marquis | ||
| 4 | DuBose, Eric | Hinch, AJ (IR) | Hansen, Dave | Lankford, Ray (IR) | Garcia, Danny (IR) | Mayne, Brent (IR) | Flaherty, John | Knotts, Gary (IR) | ||
| 5 | Garcia, Karim (IR) | Ortiz, Russ | Hidalgo, Richard | Levine, Al | Gload, Ross | McEwing, Joe | Grimsley, Jason | Murphy, Donnie | ||
| 6 | Kolb, Danny (IR) | Riedling, John | Jacobsen, Bucky (IR) | Olmedo, Ray | Hammock, Robby (IR) | Niemann, Jeff (UNC) | Guzman, Freddy (IR) | Valdez, Merkin (IR) | ||
| 7 | Martinez, Sandy (IR) | Sullivan, Scott (IR) | Ryan, Michael | Reese, Pokey (IR) | Horgan, Joe | Van Poppel, Todd | Perez, Eddie | |||
| 8 | Moreno, Orber (IR) | Thomas, Charles | Werth, Jayson | Krynzel, Dave | Williams, Gerald | |||||
| 9 | Norton, Greg (IR) | Wilson, Paul | Ojeda, Augie (IR) | Wise, DeWayne (IR) | ||||||
| 10 | Paul, Josh | Tankersley, Dennis (IR) | ||||||||
| 11 | Ransom, Cody (IR) | |||||||||
| 12 | Rodriguez, Felix | |||||||||
| 13 | Salmon, Tim (IR) | |||||||||
| 14 | ||||||||||
| 15 | ||||||||||
| Riegle (17) | Baton Rouge (18) | Puget Sound (19) | MetroMess (20) | Seattle (21) | Aliso (22) | Pnutsen (23) | Baltimore (24) | |||
| Drafted Players | 1 | David Ross | Claudio Vargas | Geoff Geary | Dennys Reyes | Darrell May | Taylor Buchholz (UNC) | Joel Guzman (UNC) | Abe Alvarez | |
| 2 | Wes Helms | Brandon Lyon | Bret Boone | Roman Colon | Doug Waechter | Miguel Ojeda | Quillermo Quiroz | John Wasdin | ||
| 3 | ||||||||||
| 4 | ||||||||||
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| 7 | ||||||||||
| Pullbacks | 1 | Alan Embree | SKIPPED | Jimmy Gobble | Josh Hancock | Ramon Martinez | Adam Melhuse | |||
| 2 | SKIPPED | Mike Adams | Ron Mahay | Terry Mulholland | ||||||
| 3 | RA Dickey | Russ Springer | ||||||||
| 4 | Ricardo Rodriguez | |||||||||
| 5 | Esteban Yan | |||||||||
| 6 | ||||||||||
| Unprotected (Draft Eligible) |
1 | Almanzar, Carlos | Bocachica, Hiram | Bautista, Danny (IR) | Biddle, Rocky (IR) | Carrasco, DJ | Bell, Rob | Kata, Matt | Blanco, Andres | |
| 2 | Brito, Juan (IR) | Good, Andrew | Davis, JJ | Brocail, Doug | Cedeno, Roger | Cabrera, Jovy (IR) | Madritsch, Bobby | Castillo, Alberto | ||
| 3 | Burke, Jamie | Grieve, Ben | Munro, Pete | Higginson, Bobby | Cerda, Jaime | Davis, Ben (IR) | Diaz, Einar | |||
| 4 | Delgado, Wilson (IR) | Lima, Jose | Patterson, Danny | Perez, Timo | Durbin, Chad (IR) | Leiter, Al | Gryboski, Kevin | |||
| 5 | Dreifort, Darren, (IR) | Neal, Blaine | Perry, Herbert | Kroeger, Josh (IR) | Mateo, Ruben (IR) | Hernandez, Jose | ||||
| 6 | Escobar, Alex (IR) | Nivar, Ramon | Ramirez, Erasmo | Mays, Joe | McKay, Cody (IR) | Hudson, Luke | ||||
| 7 | Groom, Buddy | Perisho, Matt | Randolph, Steven | Osuna, Antonio | Reed, Steve | McCarty, David | ||||
| 8 | Larkin, Barry (IR) | Relaford, Desi | Roa, Joe | Rodriguez, Eddy (IR) | Spencer, Shane (IR) | Merloni, Lou | ||||
| 9 | McLemore, Mark (IR) | Sierra, Ruben | Rueter, Kirk | Shouse, Brian | Pickering, Calvin | |||||
| 10 | Santiago, Benito | Tadano, Kazuhito | Wilson, Enrique | Seay, Bobby | ||||||
| 11 | Sparks, Steve (IR) | Takatsu, Shingo | ||||||||
| 12 | Valent, Eric | Valdez, Ismael | ||||||||