| Round 1 | ||||
| Date/Time | Number | Team | Traded From | Selection |
| 2/1/06 12:00 PM | 1 | Hens | Sluggers | Felix Hernandez |
| 2/1/06 12:30 PM | 2 | Bandits | Zach Duke | |
| 2/1/06 1:00 PM | 3 | Phobics | Jeremy Hermida | |
| 2/1/06 1:30 PM | 4 | Hysteria | Andy Marte | |
| 2/1/06 2:00 PM | 5 | Commuters | Irish | Prince Fielder |
| 2/1/06 2:30 PM | 6 | Boulders | Francisco Liriano | |
| 2/1/06 3:00 PM | 7 | Drillers | Ryan Doumit | |
| 2/1/06 3:30 PM | 8 | HiSox | Jeff Francoeur | |
| 2/1/06 4:00 PM | 9 | Commuters | Matt Cain | |
| 2/1/06 4:30 PM | 10 | Kangaroos | Huston Street | |
| 2/1/06 5:00 PM | 11 | Blues | Ervin Santana | |
| 2/1/06 5:30 PM | 12 | Beasts | Ryan Zimmerman | |
| 2/1/06 6:00 PM | 13 | Scorpions | Justin Verlander | |
| 2/1/06 6:30 PM | 14 | Peanuts | Chris Duffy | |
| 2/1/06 7:00 PM | 15 | Anarchists | Brian McCann | |
| 2/1/06 7:30 PM | 16 | Skeeters | Josh Towers | |
| 2/1/06 8:00 PM | 17 | Bandits | Buffalo Chips | Aaron Fultz |
| 2/1/06 8:30 PM | 18 | Vipers | Dan Johnson | |
| 2/1/06 9:00 PM | 19 | Phobics | Force | Conor Jackson |
| 2/1/06 9:30 PM | 20 | Drillers | Hegelians | Chien-Ming Wang |
| 2/1/06 10:00 PM | 21 | Sluggers | Hens | Anthony Reyes |
| 2/1/06 10:30 PM | 22 | Pinnipeds | Jon Papelbon | |
| 2/1/06 11:00 PM | 23 | Sidewinders | Hanley Ramirez | |
| 2/1/06 11:30 PM | 24 | Synthesis | Robinson Cano | |