| Round 1 | Round 2 | |||||||
| 1 | The New Revolution | 3/10/06 trade with the Hunters, 3/31/07 trade with the Revolution | Piazza, Mike | 1 | The Vampire Hunters | Benitez, Armando | ||
| 2 | The Flying Squirrels | 3/31/07 trade with the Squirrels | Young, Chris (OF) | 2 | The New Revolution | Matsui, Hideki | ||
| 3 | The Flying Squirrels | 3/31/07 trade with the Hunters | Lincecum, Tim | 3 | The Vanilla Mudsharks | Dempster, Ryan | ||
| 4 | The Vanilla Mudsharks | 6/12/06 trade with the I.P., 3/31/07 trade with the Squirrels | Gonzalez, Adrian | 4 | The I.P. | Jones, Chipper | ||
| 5 | Project X | Young, Chris (P) | 5 | Project X | Johjima, Kenji | |||
| 6 | FY&I | FORFEITED FOR KERRY WOOD 60 DAY DL | FORFEITED | 6 | FY&I | Guillen, Carlos | ||
| 7 | The Vampire Hunters | 3/10/06 trade with the Squirrels | Wickman, Bob | 7 | The Flying Squirrels | Dotel, Octavio | ||
| 8 | The New Revolution | 5/15/06 trade with The Lone Gunmen | Butler, Billy | 8 | The Flying Squirrels | 2/21/07 trade with the Revolution via 6/12/06 trade with The Lone Gunmen | Borowski, Joe | |
| Round 3 | Round 4 | |||||||
| 1 | The Vampire Hunters | Santana, Ervin | 1 | The Vampire Hunters | Taveras, Wily | |||
| 2 | The Lone Gunmen | 3/1/07 trade with the Clovers | Wainwright, Adam | 2 | The Flying Squirrels | Hart, Corey | ||
| 3 | The Vanilla Mudsharks | Duncan, Chris | 3 | The Vanilla Mudsharks | Kouzmanoff, Kevin | |||
| 4 | The Flying Squirrels | 6/12/06 trade with the I.P. | Torres, Salomon | 4 | The I.P. | Harang, Aaron | ||
| 5 | Project X | Barfield, Josh | 5 | Project X | Willingham, Josh | |||
| 6 | FY&I | Beltre, Adrian | 6 | FY&I | Clemens, Roger | |||
| 7 | The Flying Squirrels | Julio, Jorge | 7 | The New Revolution | Lugo, Julio | |||
| 8 | The Lone Gunmen | Soriano, Rafael | 8 | The Lone Gunmen | Iannetta, Chris | |||
| Round 5 | Round 6 | |||||||
| 8 | The Lone Gunmen | Greinke, Zack | 1 | The Vampire Hunters | Tulowitzki, Troy | |||
| 7 | The Flying Squirrels | Cabrera, Daniel | 2 | The New Revolution | Mussina, Mike | |||
| 6 | FY&I | Shealy, Ryan | 3 | The Vanilla Mudsharks | Bailey, Homer | |||
| 5 | Project X | Wheeler, Dan | 4 | The I.P. | Maybin, Cameron | |||
| 4 | The I.P. | Posada, Jorge | 5 | Project X | Kearns, Austin | |||
| 3 | The Vanilla Mudsharks | Jones, Adam | 6 | FY&I | Kinsler, Ian | |||
| 2 | The New Revolution | Prior, Mark | 7 | The Flying Squirrels | Roberts, Dave | |||
| 1 | The Vampire Hunters | Thomas, Frank | 8 | The Lone Gunmen | Braun, Ryan | |||
| Round 7 | Round 8 | |||||||
| 8 | The Lone Gunmen | Patterson, John | 1 | The Vampire Hunters | Owens, Henry | |||
| 7 | The Flying Squirrels | Otsuka, Akinori | 2 | The New Revolution | Crisp, Coco | |||
| 6 | FY&I | Perez, Oliver | 3 | The Vanilla Mudsharks | Weathers, David | |||
| 5 | Project X | Wilson, Brian | 4 | The I.P. | Overbay, Lyle | |||
| 4 | The I.P. | Jackson, Connor | 5 | Project X | James, Chuck | |||
| 3 | The Vanilla Mudsharks | Bruce, Jay | 6 | FY&I | Hermanson, Dustin | |||
| 2 | The New Revolution | Gomez, Carlos | 7 | The I.P. | 3/31/07 trade with the Flying Squirrels | McDougal, Mike | ||
| 1 | The Vampire Hunters | McCarthy, Brandon | 8 | The Lone Gunmen | Hamilton, Josh | |||
| Round 9 | Round 10 | |||||||
| 8 | The Lone Gunmen | Marte, Andy | 1 | The Vampire Hunters | Lee, Cliff | |||
| 7 | The Flying Squirrels | Howry, Bob | 2 | The New Revolution | Gonzalez, Mike | |||
| 6 | FY&I | Escobar, Kelvim | 3 | The Vanilla Mudsharks | Victorino, Shane | |||
| 5 | Project X | Hensley, Clay | 4 | The I.P. | Igawa, Kei | |||
| 4 | The I.P. | Garciaparra, Nomar | 5 | Project X | Reyes, Al | |||
| 3 | The Vanilla Mudsharks | Alou, Moises | 6 | FY&I | Gorzellany, Tom | |||
| 2 | The New Revolution | Pierzynski, A.J. | 7 | The Flying Squirrels | Crede, Joe | |||
| 1 | The Vampire Hunters | Sweeney, Mike | 8 | The Lone Gunmen | Billingsley, Chad | |||
| Round 11 | Round 12 | |||||||
| 8 | The Lone Gunmen | Crosby, Bobby | 1 | The Vampire Hunters | Varitek, Jason | |||
| 7 | The Flying Squirrels | Granderson, Curtis | 2 | The New Revolution | Kemp, Matt | |||
| 6 | FY&I | Cameron, Mike | 3 | The Vanilla Mudsharks | Garcia, Freddy | |||
| 5 | Project X | Baker, Jeff | 4 | The I.P. | Clement, Matt | |||
| 4 | The I.P. | Monroe, Craig | 5 | Project X | Garko, Ryan | |||
| 3 | The Vanilla Mudsharks | Burke, Chris | 6 | FY&I | Encarnacion, Edwin | |||
| 2 | The New Revolution | Ethier, Andre | 7 | The Flying Squirrels | Ensberg, Morgan | |||
| 1 | The Vampire Hunters | Kent, Jeff | 8 | The Lone Gunmen | Morrow, Brandon | |||
| Supplemental Picks | ||||||||
| The I.P. | Pence, Hunter | |||||||
| FY&I | Tracy, Chad | |||||||
| The Lone Gunmen | Kotchman, Casey | |||||||