| Round 1 |
| 1 | Allentown Mules | Mike Trout | OF | LAA | PHI |
| 2 | Empire City Trojans | Chris Davis | 1B | Bal | RWD |
| 3 | Saskatoon Shields | Zack Greinke | SP | LAD | PHI |
| 4 | Durham Bulls | Dustin Pedroia | C | Bos | RWD |
| Round 2 |
| 5 | Durham Bulls | Troy Tulowitzki | SS | Col | RWD |
| 6 | Saskatoon Shields | Jordan Zimmermann | SP | Was | AMI |
| 7 | Empire City Trojans | Adam Jones | CF | Bal | RWD |
| 8 | Allentown Mules | Cliff Lee | SP | Phi | RWD |
| Round 3 |
| 9 | Allentown Mules | Manny Machado | 3B | Bal | AMI |
| 10 | Empire City Trojans | Adam Wainwright | SP | StL | PHI |
| 11 | Saskatoon Shields | Justin Verlander | SP | Det | PHI |
| 12 | Durham Bulls | Cole Hamels | SP | Phi | AMI |
| Round 4 |
| 13 | Durham Bulls | Stephen Strasburg | SP | Was | RWD |
| 14 | Saskatoon Shields | Yadier Molina | C | StL | PHI |
| 15 | Empire City Trojans | Starling Marte | OF | Pit | RWD |
| 16 | Allentown Mules | Hisashi Iwakuma | SP | Sea | RWD |
| Round 5 |
| 17 | Allentown Mules | Giancarlo Stanton | OF | Mia | PHI |
| 18 | Empire City Trojans | Chris Tillman | SP | Bal | PHI |
| 19 | Saskatoon Shields | Jered Weaver | SP | LAA | AMI |
| 20 | Durham Bulls | David Wright | 3B | NYM | PHI |
| Round 6 |
| 21 | Durham Bulls | Shin-Soo Choo | OF | Tex | PHI |
| 22 | Saskatoon Shields | Jose Altuve | 2B | Hou | BOS |
| 23 | Empire City Trojans | Hunter Pence | OF | SF | RWD |
| 24 | Allentown Mules | Justin Masterson | SP | Cle | AMI |
| Round 7 |
| 25 | Allentown Mules | Craig Kimbrel | RP | Atl | AMI |
| 26 | Empire City Trojans | Clay Buchholz | SP | Bos | PHI |
| 27 | Saskatoon Shields | Chris Johnson | 3B | Atl | RWD |
| 28 | Durham Bulls | Shane Victorino | OF | Bos | RWD |
| Round 8 |
| 29 | Durham Bulls | Jacoby Ellsbury | CF | NYY | BOS |
| 30 | Saskatoon Shields | Allen Craig | 1B | StL | AMI |
| 31 | Empire City Trojans | J.J. Hardy | SS | Bal | RWD |
| 32 | Allentown Mules | Neil Walker | 2B | Pit | BOS |
| Round 9 |
| 33 | Allentown Mules | Matt Kemp | CF | LAD | AMI |
| 34 | Empire City Trojans | Steve Cishek | RP | Mia | BOS |
| 35 | Saskatoon Shields | Jon Jay | CF | StL | BOS |
| 36 | Durham Bulls | Prince Fielder | 1B | Tex | RWD |
| Round 10 |
| 37 | Durham Bulls | Pedro Alvarez | 3B | Pit | BOS |
| 38 | Saskatoon Shields | Nate Schierholtz | OF | CHC | AMI |
| 39 | Empire City Trojans | Patrick Corbin | SP | Arz | AMI |
| 40 | Allentown Mules | Mark Trumbo | 1B | Arz | BOS |
| Round 11 |
| 41 | Allentown Mules | Jarrod Saltalamacchia | C | Mia | RWD |
| 42 | Empire City Trojans | Daniel Murphy | 2B | NYM | RWD |
| 43 | Saskatoon Shields | Trevor Cahill | SP | Arz | PHI |
| 44 | Durham Bulls | Greg Holland | RP | KC | BOS |
| Round 12 |
| 45 | Durham Bulls | Drew Smyly | RP | Det | BOS |
| 46 | Saskatoon Shields | Casey Janssen | RP | Tor | PHI |
| 47 | Empire City Trojans | Jason Grilli | RP | Pit | AMI |
| 48 | Allentown Mules | Andre Ethier | SP | LAD | AMI |
| Round 13 |
| 49 | Allentown Mules | Andrelton Simmons | 3B | Atl | BOS |
| 50 | Empire City Trojans | Miguel Montero | SP | Arz | BOS |
| 51 | Saskatoon Shields | Alcides Escobar | SP | KC | AMI |
| 52 | Durham Bulls | Jose Quintana | SP | CHW | BOS |
| Round 14 |
| 53 | Durham Bulls | Mat Garza | SP | Tex | PHI |
| 54 | Saskatoon Shields | Albert Pujols | 1B | LAA | PHI |
| 55 | Empire City Trojans | Rafael Soriano | RP | TB | BOS |
| 56 | Allentown Mules | Travis Wood | SP | Sea | RWD |
| Round 15 |
| 57 | Allentown Mules | Ryan Cook | RP | Mia | PHI |
| 58 | Empire City Trojans | Aramis Ramirez | 3B | Mil | AMI |
| 59 | Saskatoon Shields | Jesse Crain | RP | LAA | AMI |
| 60 | Durham Bulls | Austin Jackson | CF | Det | PHI |
| Round 16 |
| 61 | Durham Bulls | Joe Nathan | RP | Tex | PHI |
| 62 | Saskatoon Shields | J.J. Putz | RP | Hou | RWD |
| 63 | Empire City Trojans | Jarrod Parker | SP | Oak | AMI |
| 64 | Allentown Mules | Adam Lind | 1B | Tor | AMI |
| Round 17 |
| 65 | Allentown Mules | Jake McGee | RP | TB | PHI |
| 66 | Empire City Trojans | Dayan Viciedo | OF | CHW | AMI |
| 67 | Saskatoon Shields | Yovani Gallardo | SP | Mil | RWD |
| 68 | Durham Bulls | Dan Straily | SP | Oak | RWD |
| Round 18 |
| 69 | Durham Bulls | Matt Adams | 1B | StL | AMI |
| 70 | Saskatoon Shields | Tim Collins | RP | StL | PHI |
| 71 | Empire City Trojans | Vinnie Pestano | RP | Bal | AMI |
| 72 | Allentown Mules | Michael Saunders | OF | Sea | RWD |
| Round 19 |
| 73 | Allentown Mules | Mark Buehrle | SP | Tor | BOS |
| 74 | Empire City Trojans | C.C. Sabathia | SP | NYY | RWD |
| 75 | Saskatoon Shields | Justin Smoak | 1B | Sea | AMI |
| 76 | Durham Bulls | Howie Kendrick | 2B | LAA | PHI |
| Round 20 |
| 77 | Durham Bulls | Tim Hudson | SP | SF | AMI |
| 78 | Saskatoon Shields | Adam Eaton | OF | CHW | BOS |
| 79 | Empire City Trojans | Ian Kennedy | SP | SD | BOS |
| 80 | Allentown Mules | Martin Prado | 3B | Arz | BOS |
|