Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2010 Club |
| 1 | Josh Rodriguez | SS | Pittsburgh | Cleveland | Columbus |
| 2 | Jose Flores | RHP | Seattle | Cleveland | Columbus |
| 3 | Joe Paterson | LHP | Arizona | San Francisco | Fresno |
| 4 | Adrian Rosario | RHP | Baltimore | Milwaukee | Nashville |
| 5 | Nathan Adcock | RHP | Kansas City | Pittsburgh | Indianapolis |
| 6 | Elvin Ramirez | RHP | Washington | New York (NL) | Buffalo |
| 7* | Mason Tobin | RHP | Chicago (NL) | Los Angeles (AL) | Salt Lake |
| 8 | Aneury Rodriguez | RHP | Houston | Tampa Bay | Durham |
| 9 | Patrick Egan | RHP | Milwaukee | Baltimore | Norfolk |
| 10 | Bradley Emaus | 2B | New York (NL) | Toronto | Las Vegas |
| 11 | George Kontos | RHP | San Diego | New York (AL) | Scranton/Wilkes-Barre |
| 12 | Scott Diamond | LHP | Minnesota | Atlanta | Gwinnett |
| 13 | Robert Fish | LHP | New York (AL) | Los Angeles (AL) | Salt Lake |
| 14 | Cesar Cabral | LHP | Tampa Bay | Boston | Pawtucket |
| 15 | Michael Martinez | IF | Philadelphia | Washington | Syracuse |
| 16 | Brian Broderick | RHP | Washington | St. Louis | Memphis |
| 17 | Lance Pendleton | RHP | Houston | New York (AL) | Scranton/Wilkes-Barre |
| 18 | Pedro Beato | RHP | New York (NL) | Baltimore | Norfolk |
| 19 | Daniel Turpen | RHP | New York (AL) | Boston | Pawtucket |
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2010 Club |
| 1 | Bradley Chalk | OF | Pittsburgh | San Diego | San Antonio |
| 2 | Jose Rivero | OF | Arizona | Seattle | West Tenn |
| 3 | Dale Mollenhauer | 2B | Baltimore | Chicago (AL) | Birmingham |
| 4 | Heath Rollins | RHP | Kansas City | Tampa Bay | Montgomery |
| 5 | Michael Allen | RHP | Washington | Minnesota | New Britain |
| 6 | Ronny Morla | RHP | New York (NL) | Chicago (NL) | Tennessee |
| 7 | Jaime Ortiz | IF | Florida | Los Angeles (NL) | Chattanooga |
| 8 | Daniel Sattler | RHP | Los Angeles (AL) | Oakland | Midland |
| 9 | Jeiler Castillo | RHP | Oakland | Houston | Corpus Christi |
| 10 | Ivan Contreras | 2B | Toronto | Los Angeles (AL) | Arkansas |
| 11 | Jean Mijares | LHP | St. Louis | Minnesota | New Britain |
| 12 | Jacob Blackwood | 3B | Jacob Blackwood | San Francisco | Richmond |
| 13 | Fausto Mier | C | Fausto Mier | Los Angeles (NL) | Chattanooga |
| 14 | Eliecer Cardenas | RHP | Atlanta | Minnesota | New Britain |
| 15 | Justin Dowdy | LHP | San Francisco | Tampa Bay | Montgomery |
| 16 | Christopher Frey | OF | Philadelphia | Colorado | Tulsa |
| 17 | Travis Scott | C | Pittsburgh | Los Angeles (AL) | Arkansas |
| 18 | Casey Lambert | LHP | Baltimore | Chicago (NL) | Tennessee |
| 19 | Richard Brooks | RHP | New York (NL) | Chicago (AL) | Birmgingham |
| 20 | Starling De La Rosa | LHP | Texas | Kansas City | NW Arkansas |
| 21 | Rowdy Hardy | LHP | Atlanta | Kansas City | NW Arkansas |
| 22 | Dashenko Ricardo | C | San Francisco | Baltimore | Bowie |
| 23 | Justin Friend | RHP | Philadelphia | Oakland | Midland |
| 24 | Matthew Sartor | RHP | San Francisco | Los Angeles (NL) | Chattanooga |
Double-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2010 Club |
| 1 | Jacob Rasner | RHP | Baltimore | Chicago (AL) | Winston-Salem |
| 2 | Quintin Berry | OF | New York (NL) | San Diego | Lake Elsinore |
| 3 | Brent Allar | RHP | Florida | Baltimore | Frederick |
| 4 | Roan Salas | IF | Toronto | Tampa Bay | VSL Rays |
Minors