Draft Order
| 01. Houston |
| 02. Chicago-NL |
| 03. Colorado |
| 04. Minnesota |
| 05. Cleveland |
| 06. Miami |
| 07. Boston |
| 08. Kansas City |
| 09. Pittsburgh — For failure to sign Mark Appel |
| 10. Toronto |
| 11. New York-NL |
| 12. Seattle |
| 13. San Diego |
| 14. Pittsburgh |
| 15. Arizona |
| 16. Philadelphia |
| 17. Chicago-AL |
| 18. Los Angeles-NL |
| 19. St. Louis |
| 20. Detroit |
| 21. Tampa Bay |
| 22. Baltimore |
| 23. Texas |
| 24. Oakland |
| 25. San Francisco |
| 26. New York-AL |
| 27. Cincinnati |
First-Round Compensation
| 28. St. Louis — For loss of Kyle Lohse |
| 29. Tampa Bay — For loss of B.J. Upton |
| 30. Texas — For loss of Josh Hamilton |
| 31. Atlanta — For loss of Michael Bourn |
| 32. New York-AL — For loss of Nick Swisher |
| 33. New York-AL — For loss of Rafael Soriano |
Competitive Balance Lottery Round A
| 34. Kansas City |
| 35. Miami — From Pittsburgh |
| 36. Arizona |
| 37. Baltimore |
| 38. Cincinnati |
| 39.Detroit — From Miami in Anibal Sánchez trade |