July 11th, 2006 @ 8:00PM ET |
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| Rd | Pick | Team | Selection |
| 1 | 1 | WEY (from BYE) | Justin Upton (OF - Ari) |
| 1 | 2 | TKO (from GLD) | Alex Gordon (3B - KC) |
| 1 | 3 | LV (from BRW) | Homer Bailey (P - Cin) |
| 1 | 4 | RAK (from TIJ) | Phillip Hughes (P - NYY) |
| 1 | 5 | QC (from TKO) | Troy Tulowitzki (SS - Col) |
| 1 | 6 | LV (from PEO) | Matt Garza (P - Min) |
| 1 | 7 | RAK (from LV) | Mike Pelfrey (P - NYM) |
| 1 | 8 | WEY | Nick Adenhart (P - LAA) |
| 1 | 9 | WS | Jeff Clement (C - Sea) |
| 1 | 10 | LV (from BIZ) | Cameron Maybin (OF - Det) |
| 1 | 11 | QC | Jose Tabata (OF - NYY) |
| 1 | 12 | RAK | Yovani Gallardo (P - Mil) |
| 2 | 1 | BIZ | Scott Elbert (P - LAD) |
| 2 | 2 | TKO (from PEO) | Elvis Andrus (SS - Atl) |
| 2 | 3 | LV (from GLD) | Jay Bruce (OF - Cin) |
| 2 | 4 | TKO | John Danks (P - Tex) |
| 2 | 5 | QC (from TIJ) | Kevin Slowey (P - Min) |
| 2 | 6 | QC | Brandon Erbe (P - ChC) |
| 2 | 7 | WEY (from LV) | Mark Pawelek (P - ChC) |
| 2 | 8 | WS | Gio Gonzalez (P - Phi) |
| 2 | 9 | LV (from RAK) | Hunter Pence (OF - Hou) |
| 2 | 10 | WEY | Ryan Braun (3B - Mil) |
| 2 | 11 | TKO (from BRW) | Michael Bowden (P - Bos) |
| 2 | 12 | WEY (from BYE) | Humberto Sanchez (P - Det) |