Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2008 Club |
| 1 | Terrell Young | RHP | Washington | Cincinnati | Sarasota |
| 2 | Reegie Corona | INF | Seattle | New York (AL) | Trenton |
| 3 | Everth Cabrera | SS | San Diego | Colorado | Asheville |
| 4 | Donald Veal | LHP | Pittsburgh | Chicago (NL) | Tennessee |
| 5 | Lou Palmisano | C | Baltimore* | Milwaukee | Brevard County |
| 6 | Luis Perdomo | RHP | San Francisco | St. Louis | Springfield |
| 7 | David Patton | RHP | Cincinnati** | Colorado | Modesto |
| 8 | Kyle Bloom | LHP | Detroit | Pittsburgh | Altoona |
| 9 | Jose Lugo | LHP | Kansas City*** | Minnesota | Ft. Myers |
| 10 | Benjamin Copeland | CF | Oakland | San Francisco | Fresno |
| 11 | James Skelton | C | Arizona | Detroit | Erie |
| 12 | Zachary Kroenke | LHP | Florida | New York (AL) | Scranton/Wilkes-Barre |
| 13 | Gilbert De La Vara | LHP | Houston | Kansas City | Northwest Arkansas |
| 14 | Jason Jones | RHP | Minnesota | New York (AL) | Scranton/Wilkes-Barre |
| 15 | Darren O'Day | RHP | New York (NL) | Los Angeles (AL) | Salt Lake |
| 16 | Eddie Morlan | RHP | Milwaukee | Tampa Bay | Montgomery |
| 17 | Robert Mosebach | RHP | Philadelphia | Los Angeles (AL) | Arkansas |
| 18 | Miguel Gonzalez | RHP | Boston | Los Angeles (AL) | DNP |
| 19 | Derek Rodriguez | RHP | Tampa Bay | Chicago (AL) | Charlotte |
| 20 | Ivan Nova | RHP | San Diego | New York (AL) | Tampa |
| 21 | Rocky Cherry | RHP | New York (NL) | Baltimore | Norfolk |
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2008 Club |
| 1 | Ricardo Nanita | OF | Syracuse (WAS) | Chicago (AL) | Birmingham |
| 2 | Ryan Patrick | RHP | Tacoma (SEA) | Milwaukee | Huntsville |
| 3 | Andres Santos | LHP | Indianapolis (PIT) | New York (AL) | DSL Yankees |
| 4 | Robert Valido | SS | Norfolk (BAL) | Chicago (AL) | Charlotte |
| 5 | Matt Yourkin | LHP | Fresno (SF) | Florida | Carolina |
| 6 | Francisco Lizarraga | SS | Louisville (CIN) | Los Angeles (NL) | Las Vegas |
| 7 | Luis Ortega | RHP | Omaha (KC) | Washington | DSL Nationals |
| 8 | Yusuf Carter | OF | Sacramento (OAK) | Chicago (NL) | Daytona |
| 9 | Elio Sarmiento | C | Oklahoma City (TEX) | San Francisco | San Jose |
| 10 | Anthony Hatch | INF | Albuquerque (LAD) | Toronto | New Hamp. |
| 11 | Ryan Klosterman | SS | New Orleans (FLA) | Toronto | New Hamp. |
| 12 | Russ Haltiwanger | RHP | Memphis (STL) | Kansas City | NW Arkansas |
| 13 | Cody Haerther | OF | Las Vegas (TOR) | St. Louis | Memphis |
| 14 | Andrew Locke | RF | Round Rock (HOU) | Los Angeles (NL) | Inland Empire |
| 15 | Henry Arias | RHP | Rochester (MIN) | Cincinnati | Dayton |
| 16 | Carl Loadenthal | OF | Buffalo (NYM) | Atlanta | Richmond |
| 17 | Mark Holliman | RHP | Nashville (MIL) | Chicago (NL) | Tennessee |
| 18 | Kyle Haines | 2B | Lehigh Valley (PHI) | San Francisco | Connecticut |
| 19 | Jason Rice | RHP | Pawtucket (BOS) | Chicago (AL) | Kannapolis |
| 20 | Rafael Quintero | RHP | Indianapolis (PIT) | Cleveland | DSL Indians |
| 21 | Josh Perrault | RHP | Norfolk (BAL) | Washington | Harrisburg |
| 22 | Richard Suomi | C | Omaha (KC) | Philadelphia | Lehigh Valley |
| 23 | Josue Selenes | RHP | Sacramento (OAK) | New York (AL) | Staten Island |
| 24 | Guilder Rodriguez | SS | Oklahoma (TEX) | Milwaukee | Huntsville |
| 25 | Brett Harker | RHP | New Orleans (FLA) | Philadelphia | Reading |
| 26 | David Shinskie | RHP | Las Vegas (TOR) | Minnesota | New Britain |
| 27 | John Madden | RHP | Buffalo (NYM) | San Diego | Portland |
| 28 | Jonathan Ash | 2B | Nashville (MIL) | Houston | Round Rock |
| 29 | Javis Diaz | OF | Lehigh Valley (PHI) | San Diego | Lake Elsinore |
| 30 | Miguel Marquez | RHP | Pawtucket (BOS) | Seattle | DNP |
| 31 | Gerardo Esparza | RHP | Indianapolis (PIT) | Seattle | VSL Mariners |
| 32 | Carlos Arias | RHP | Omaha (KC) | Cleveland | Mah. Valley |
| 33 | Ronald Hill | RHP | New Orleans (FLA) | Philadelphia | Reading |
| 34 | Shane Justis | SS | Nashville (MIL) | Los Angeles (NL) | Jacksonville |
| 35 | Juan Sanchez | SS | Nashville (MIL) | Milwaukee | GCL Twins |
Double-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2008 Club |
| 1 | Andrew Barb | RHP | Bowie (BAL) | Seattle | DNP |
Minors