Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2009 Club |
| 1 | Jamie Hoffmann* | OF | Washington | Los Angeles (NL) | Albuquerque |
| 2 | John Raynor | OF | Pittsburgh | Florida | New Orleans |
| 3 | Benjamin Snyder** | LHP | Baltimore | San Francisco | Connecticut |
| 4 | Edgar Osuna | LHP | Kansas City | Atlanta | Mississippi |
| 5 | Hector Ambriz | RHP | Cleveland | Arizona | Reno |
| 6 | Zachary Kroenke | LHP | Arizona | New York (AL) | Scranton/WB |
| 7 | Carlos Monasterios | RHP | New York (NL) | Philadelphia | Reading |
| 8 | Jorge Jimenez*** | 3B | Houston | Boston | Portland |
| 9 | Robert Cassevah | RHP | Oakland | Los Angeles (AL) | Arkansas |
| 10 | Zechry Zinicola | RHP | Toronto | Washington | Syracuse |
| 11 | Chuck Lofgren | LHP | Milwaukee | Cleveland | Columbus |
| 12 | Michael Parisi | RHP | Chicago (NL) | St. Louis | Memphis |
| 13 | Armando Zerpa | LHP | Tampa Bay | Boston | Salem |
| 14 | Kanekoa Texeira | RHP | Seattle | New York (AL) | Trenton |
| 15 | Steven Johnson | RHP | San Francisco | Baltimore | Bowie |
| 16 | Ben Jukich | LHP | St. Louis | Cincinnati | Louisville |
| 17 | David Herndon | RHP | Philadelphia | Los Angeles (AL) | Arkansas |
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2009 Club |
| 1 | Arismendy Mota | RHP | Syracuse (WAS) | Chicago (AL) | DSL White Sox |
| 2 | Rodolfo Cardona | SS | Indianapolis (PIT) | Baltimore | Delmarva |
| 3 | Jose Duran | RHP | Norfolk (BAL) | Houston | Lancaster |
| 4 | Brian Horwitz | OF | Columbus (CLE) | San Francisco | Fresno |
| 5 | John Lujan | RHP | Buffalo (NYM) | Chicago (AL) | Birmingham |
| 6 | Beau Vaughan | RHP | Sacramento (OAK) | Texas | Frisco |
| 7 | Ruben De La Rosa | RHP | Las Vegas (TOR) | Washington | GCL Nationals |
| 8 | Miguel Sierra | RHP | Durham (TB) | Chicago (NL) | AZL Cubs |
| 9 | Terrence Engles | RHP | Tacoma (SEA) | Washington | Potomac |
| 10 | James Tomlin | OF | Oklahoma (TEX) | Los Angeles (NL) | Chattanooga |
| 11 | Anillins Martinez | LHP | New Orleans (FLA) | Cleveland | Lake County |
| 12 | Jake Stevens | LHP | Fresno (SF) | Baltimore | Frederick |
| 13 | Matt Meyer | LHP | Memphis (STL) | Cleveland | Columbus |
| 14 | Angelo Sanchez | RHP | Lehigh Valley (PHI) | Minnesota | Elizabethton |
| 15 | Michael Wlodarczyk | LHP | Syracuse (WAS) | Tampa Bay | Durham |
| 16 | Marshall Hubbard | 1B | Buffalo (NYM) | Seattle | West Tenn |
| 17 | Andrew Jenkins | C | Oklahoma (TEX) | Florida | Jacksonville |
| 18 | Nicholas Moresi | OF | Syracuse (WAS) | Houston | Corpus Christi |
| 19 | Rolando Valdez | RHP | Buffalo (NYM) | San Diego | San Antonio |
| 20 | Winston Marquez | LHP | Oklahoma (TEX) | Minnesota | Beloit |
| 21 | Orlando Lara | LHP | Buffalo (NYM) | San Diego | Mexico |
Double-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2009 Club |
| 1 | Johan Figuereo | RHP | Binghamton (NYM) | Washington | Vermont |
| 2 | Hayden Beard | RHP | San Antonio (SD) | New York (NL) | Did not play |
| 3 | Douglas Salinas | RHP | Carolina (CIN) | Tampa Bay | Hudson Valley |
| 4 | Raul Burgos | RHP | Chattanooga (LAD) | San Francisco | AZL Giants |
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