| 1st Round | 4th Round | ||
| 1. Dustin Ackley | Houston Astros | 91. Jose Arredondo | Boston Red Sox |
| 2. Mike Moustakas | Chicago White Sox | 92. Matt Carpenter | Chicago Cubs |
| 3. Paul Goldschmidt | Washington Nationals | 93. Charlie Blackmon | Minnesota Twins |
| 4. Johnny Giavotella | Boston Red Sox | 94. Dave Sappelt | San Diego Padres |
| 5. Zack Cozart | Boston Red Sox | 95. Brett Pill | Detroit Tigers |
| 6. Anthony Rizzo | Colorado Rockies | 96. James Darnell | Arizona Diamondbacks |
| 7. Lonnie Chisenhall | Cleveland Indians | 97. Ivan De Jesus | St. Louis Cardinals |
| 8. Alejandro De Aza | Oakland A's | 98. Carlos Peguero | Arizona Diamondbacks |
| 9. Salvador Perez | Seattle Mariners | 99. Mike Nickeas | New York Mets |
| 10. Josh Collmenter | Texas Rangers | 100. Rich Thompson | Toronto Blue Jays |
| 11. Jerry Sands | Los Angeles Angels | 101. Eduardo Escobar | Philadelphia Phillies |
| 12. Drew Pomeranz | Boston Red Sox | 102. Rafael Perez | Los Angeles Dodgers |
| 13. J.D. Martinez | Washington Nationals | 103. Pedro Beato | New York Mets |
| 14. Randall Delgado | Arizona Diamondbacks | 104. Josh Spence | Baltimore Orioles |
| 15. Henderson Alvarez | St. Louis Cardinals | 105. J.B. Shuck | Baltimore Orioles |
| 16. Jose Altuve | Tampa Bay Rays | 106. Kyle Weiland | Tampa Bay Rays |
| 17. Jimmy Paredes | Baltmore Orioles | 107. Jeff Locke | St. Louis Cardinals |
| 18. Blake Beavan | Cleveland Indians | 108. Austin Romine | Kansas City Royals |
| 19. Danny Duffy | Seattle Mariners | 109. Anthony Swarzak | Los Angeles Dodgers |
| 20. Arodys Vizcaino | New York Mets | 110. Brandon Laird | St. Louis Cardinals |
| 21. Ryan Lavarnway | Chicago White Sox | 111. Michael Fiers | Minnesota Twins |
| 22. Nathan Eovaldi | New York Mets | 112. Russ Canzler | Cleveland Indians |
| 23. Eric Thames | San Francisco Giants | 113. Bryan Shaw | Los Angeles Angels |
| 24. Alex Liddi | Seattle Mariners | 114. Aneury Rodriguez | Detroit Tigers |
| 25. Dellin Betances | Chicago Cubs | 115. Louis Coleman | Texas Rangers |
| 26. Chris Parmalee | Atlanta Braves | 116. Chris Stewart | Milwaukee Brewers |
| 27. Ryan Vogelsong | Colorado Rockies | 117. Jordan Pacheco | New York Yankees |
| 28. Javy Guerra | Cincinnati Reds | 118. Zack McAllister | Colorado Rockies |
| 29. Mike Carp | Cleveland Indians | 119. Michael Martinez | Arizona Diamondbacks |
| 30. Greg Holland | Milwaukee Brewers | 120. Tsuyoshi Nishioka | Atlanta Braves |
| 2nd Round | 5th Round | ||
| 31. Addison Reed | Houston Astros | 121. Juan Cruz | Tampa Bay Rays |
| 32. Kyle Seager | Atlanta Braves | 122. Joe Paterson | Arizona Diamondbacks |
| 33. Liam Hendricks | Atlanta Braves | 123. LaTroy Hawkins | Kansas City Royals |
| 34. Cristhian Martinez | Cincinnati Reds | 124. Henry Sosa | Atlanta Braves |
| 35. Bryan Peterson | Toronto Blue Jays | 125. Luis Perez | Toronto Blue Jays |
| 36. Brian Bogusevic | Philadelphia Phillies | 126. Elliot Johnson | Colorado Rockies |
| 37. Taylor Green | Chicago Cubs | 127. Dylan Axelrod | Cincinnati Reds |
| 38. Michael Taylor | Oakland A's | 128. Eric Farris | San Diego Padres |
| 39. Garrett Richards | Seattle Mariners | 129. D.J. LeMahieu | Seattle Mariners |
| 40. Rubby de la Rosa | Washington Nationals | 130. Justin Ruggiano | Los Angeles Dodgers |
| 41. Hector Noesi | Arizona Diamondbacks | 131. Andrew Carignan | Philadelphia Phillies |
| 42. Bartolo Colon | Florida Marlins | 132. Jose Constanza | Los Angeles Dodgers |
| 43. Lance Lynn | Texas Rangers | 133. Mike MacDougal | Arizona Diamondbacks |
| 44. Jack Hannahan | Texas Rangers | 134. Chris Marrero | Washington Nationals |
| 45. Collin Cowgill | Baltimore Orioles | 135. Edgmer Escalona | Baltimore Orioles |
| 46. Juan Nicasio | Tampa Bay Rays | 136. Chance Ruffin | Tampa Bay Rays |
| 47. Aaron Crow | Seattle Mariners | 137. Mike Gonzalez | Florida Marlins |
| 48. Jim Johnson | Kansas City Royals | 138. Cory Wade | Kansas City Royals |
| 49. Endy Chavez | Milwaukee Brewers | 139. Brayan Villarreal | Los Angeles Angels |
| 50. Rex Brothers | St. Louis Cardinals | 140. Jack Cust | Florida Marlins |
| 51. Tony Campana | New York Yankees | 141. Brandon Gomes | Chicago White Sox |
| 52. Alex Cobb | Toronto Blue Jays | 142. David Carpenter | Arizona Diamondbacks |
| 53. Andy Dirks | San Francisco Giants | 143. Jason Grilli | San Francisco Giants |
| 54. Trayvon Robinson | Chicago White Sox | 144. Jeremy Moore | Detroit Tigers |
| 55. Al Albuqerque | Minnesota Twins | 145. Ryan Adams | Florida Marlins |
| 56. Tyler Chatwood | Philadelphia Phillies | 146. Cesar Ramos | San Francisco Giants |
| 57. Tony Cruz | St. Louis Cardinals | 147. Josh Donaldson | New York Yankees |
| 58. Tom Milone | Colorado Rockies | 148. Alex Burnett | Arizona Diamondbacks |
| 59. Logan Forsythe | San Diego Padres | 149. Robinson Chirinos | San Diego Padres |
| 60. Hector Sanchez | Minnesota Twins | 150. Steve Clevinger | Philadelphia Phillies |
| 3rd Round | |||
| 61. Steve Cishek | Milwaukee Brewers | ||
| 62. Eric Surkamp | Chicago White Sox | ||
| 63. Daniel McCutchen | Arizona Diamondbacks | ||
| 64. Bryan LaHair | Texas Rangers | ||
| 65. Brandon Crawford | Cincinnati Reds | ||
| 66. Todd Frazier | Cincinnati Reds | ||
| 67. Anthony Bass | San Diego Padres | ||
| 68. Ezequiel Carrera | Detroit Tigers | ||
| 69. Logan Schafer | New York Mets | ||
| 70. Tom Wilhemsen | St. Louis Cardinals | ||
| 71. Kelvin Herrera | Philadelphia Phillies | ||
| 72. Charlie Furbush | New York Yankees | ||
| 73. Brad Hand | Minnesota Twins | ||
| 74. Josh Harrison | Los Angeles Angels | ||
| 75. Scott Elbert | Los Angeles Angels | ||
| 76. Dustin McGowan | Philadelphia Phillies | ||
| 77. Blake Wood | St. Louis Cardinals | ||
| 78. Alex White | Kansas City Royals | ||
| 79. Steve Lombardozzi | Colorado Rockies | ||
| 80. Chase d'Arnaud | Washington Nationals | ||
| 81. Greg Dobbs | Chicago Cubs | ||
| 82. Wade Miley | Chicago White Sox | ||
| 83. Tim Collins | San Francisco Giants | ||
| 84. Brandon Guyer | Tampa Bay Rays | ||
| 85. Nick Hagadone | Minnesota Twins | ||
| 86. Alexander Torres | Atlanta Braves | ||
| 87. Justin Sellers | Milwaukee Brewers | ||
| 88. Alexi Amarista | Atlanta Braves | ||
| 89. Fautino de los Santos | New York Yankees | ||
| 90. Tim Federowicz | Washington Nationals |