Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2012 Club |
| 1 | Josh Fields | RHP | Houston | Boston | Pawtucket |
| 2 | Hector Rondon | RHP | Chicago (NL) | Cleveland | Akron |
| 3 | Daniel Rosenbaum | LHP | Colorado | Washington | Harrisburg |
| 4 | Ryan Pressly | RHP | Minnesota | Boston | Portland |
| 5 | Chris McGuiness | 1B | Cleveland | Texas | Frisco |
| 6 | Alfredo Silverio | OF | Miami | Los Angeles (NL) | None |
| 7 | Jeff Kobernus* | 2B | Boston | Washington | Harrisburg |
| 8 | Kyle Lobstein** | LHP | New York (NL) | Tampa Bay | Montgomery |
| 9 | Starling Peralta | RHP | Arizona | Chicago (NL) | Peoria |
| 10 | Ender Inciarte | OF | Philadelphia | Arizona | Visalia |
| 11 | Angel Sanchez | IF | Chicago (AL) | Los Angeles (AL) | Oklahoma City |
| 12 | T.J. McFarland | LHP | Baltimore | Cleveland | Columbus |
| 13 | Coty Woods | RHP | Texas | Colorado | Colorado Springs |
| 14 | Nate Freiman | 1B | Houston | San Diego | San Antonio |
| 15 | Braulio Lara | LHP | Miami | Tampa Bay | Charlotte |
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2012 Club |
| 1 | Michael Burgess | OF | Houston | Chicago (NL) | Tennessee |
| 2 | Mark Sobolewski | 3B | Minnesota | Toronto | Las Vegas |
| 3 | Tyler Kehrer | LHP | Miami | Los Angels (AL) | Inland Empire |
| 4 | Jack McGeary | LHP | Boston | Washington | Auburn |
| 5 | Sawyer Carroll | OF | Toronto | San Diego | Tucson |
| 6 | Eric Farris | 2B | Seattle | Milwaukee | Milwaukee |
| 7 | Diego Goris | 3B | San Diego | Kansas City | Idaho Falls |
| 8 | Ethan Hollingsworth | RHP | Pittsburgh | Kansas City | Omaha |
| 9 | Brendan Lafferty | LHP | Philadelphia | Kansas City | NW Arkansas |
| 10 | Elevys Gonzalez | IF | Los Angeles (NL) | Pittsburgh | Altoona |
| 11 | Matt Cerda | 3B | St. Louis | Chicago (NL) | Tennessee |
| 12 | Eliezer Mesa | OF | Detroit | Oakland | Stockton |
| 13 | Robbie Widlansky | OF | Los Angeles (AL) | Baltimore | Bowie |
| 14 | Tom Boleska | RHP | Baltimore | Minnesota | None |
| 15 | Marquez Smith | 3B | Texas | Cincinnati | Portland |
| 16 | Thomas Mendonca | 3B | Oakland | Texas | Round Rock |
| 17 | Scott Shuman | RHP | San Francisco | Tampa Bay | Montgomery |
| 18 | Ryan Dennick | LHP | Cincinnati | Kansas City | NW Arkansas |
| 19 | Cameron Lamb | RHP | Houston | San Francisco | Salem-Keizer |
| 20 | Jon Bachanov | RHP | Boston | Chicago (AL) | Birmingham |
| 21 | Alvido Jimenez | RHP | Toronto | Chicago (NL) | AZL Cubs |
| 22 | Federico Castaneda | RHP | San Diego | Kansas City | Mexico |
| 23 | Hector Nelo | RHP | Los Angeles (NL) | Washington | Harrisburg |
| 24 | Jay Voss | LHP | St. Louis | Detroit | Erie |
| 25 | Steven Hill | C | Oakland | St. Louis | St. Louis |
| 26 | Michael Gilmartin | 2B | Cincinnati | Oakland | Stockton |
| 27 | Efrain Nieves | LHP | Toronto | Detroit | Connecticut |
Double-A Phase
No players selected
Minors