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Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2007 Club |
| 1 | Tim Lahey | RHP | Tampa Bay * | Minnesota | Rochester |
| 2 | Evan Meek | RHP | Pittsburgh | Tampa Bay | Montgomery |
| 3 | Randor Bierd | RHP | Baltimore | Detroit | Erie |
| 4 | Jose Capellan | LHP | San Francisco | Boston | Lowell |
| 5 | Carlos Guevara | RHP | Florida ** | Cincinnati | Chattanooga |
| 6 | Sergio Valenzuela | RHP | Cincinnati | Atlanta | Rome |
| 7 | Matt Whitney | 3B | Washington | Cleveland | Rome |
| 8 | Wesley Wright | LHP | Houston | Los Angeles (NL) | Jacksonville |
| 9 | Fernando Hernandez | RHP | Oakland | Chicago (AL) | Birmingham |
| 10 | Brian Barton | OF | St. Louis | Cleveland | Buffalo |
| 11 | Randy Wells | RHP | Toronto | Chicago (NL) | Iowa |
| 12 | R.A. Dickey | RHP | Seattle | Minnesota | Iowa |
| 13 | Steven Register | RHP | New York (NL) | Colorado | Tulsa |
| 14 | Michael Gardner | RHP | San Diego | New York (AL) | Trenton |
| 15 | Travis Blackley | LHP | Philadelphia | San Francisco | Fresno |
| 16 | Garrett Guzman | OF | Washington | Minnesota | New Britain |
| 17 | Callix Crabbe | 2B | San Diego | Milwaukee | Nashville |
| 18 | Lincoln Holdzkom | RHP | Philadelphia | Boston | Pawtucket |
** Acquired by San Diego in exchange for cash considerations
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2007 Club |
| 1 | Rashad Eldridge | OF | Durham (TB) | Minnesota | New Britain |
| 2 | Josh Hill | RHP | Indianapolis (PIT) | Minnesota | New Britain |
| 3 | Ray Liotta | LHP | Omaha (KC) | Chicago (AL) | Winston-Salem |
| 4 | Ryan Rodriguez | LHP | Norfolk (BAL) | Chicago (AL) | Winston-Salem |
| 5 | Juan Ciriaco | SS | Fresno (SF) | San Diego | Lake Elsinore |
| 6 | Smelin Perez | SS | Albuquerque (FLA) | Pittsburgh | State College |
| 7 | Juan Apodaca | C | Louisville (CIN) | Los Angeles (NL) | Great Lakes |
| 8 | Santo Luis | RHP | Charlotte (CWS) | Houston | Lexington |
| 9 | Giuseppe Norrito | RHP | Round Rock (HOU) | Los Angeles (NL) | Jacksonville |
| 10 | Levi Romero | RHP | Oklahoma (TEX) | Houston | N/A |
| 11 | Jose Fragoso | RHP | Sacramento (OAK) | Detroit | Oneonta |
| 12 | Victor Garate | LHP | Las Vegas (LAD) | Houston | Tri-City |
| 13 | Joe Bateman | RHP | Nashville (MIL) | San Francisco | Connecticut |
| 14 | Marcos Cabral | SS | Syracuse (TOR) | Washington | Hagerstown |
| 15 | Juan Cedeno | LHP | Toledo (DET) | Washington | Wichita |
| 16 | Garry Bakker | RHP | New Orleans (NYM) | Chicago (AL) | Winston-Salem |
| 17 | Gabe DeHoyos | RHP | Portland (SD) | Kansas City | Wichita |
| 18 | Patrick Sellers | 3B | Ottawa (PHI) | Houston | Corpus Christi |
| 19 | Bo Hall | RHP | Scranton/WB (NYY) | Milwaukee | Huntsville |
| 20 | Julio Puentes | RHP | Durham (TB) | Houston | VSL Astros |
| 21 | Mauricio Mendez | RHP | Indianapolis (PIT) | Boston | GCL Red Sox |
| 22 | Tim Brown | 1B | Norfolk (BAL) | San Diego | San Antonio |
| 23 | Daron Roberts | OF | Albuquerque (FLA) | Chicago (AL) | Winston-Salem |
| 24 | Dustin Majewski | OF | Oklahoma (TEX) | Toronto | New Hampshire |
| 25 | Jose Rojas | RHP | Sacramento (OAK) | Cincinnati | Sarasota |
| 26 | Richard Campbell | RHP | Nashville (MIL) | Washington | Harrisburg |
| 27 | Brant Colamarino | 1B | Syracuse (TOR) | Oakland | Sacramento |
| 28 | Benjamin Fritz | RHP | Toledo (DET) | Oakland | Midland |
| 29 | Kurt Isenberg | LHP | Portland (SD) | Toronto | New Hampshire |
| 30 | Luke Appert | 2B | Ottawa (PHI) | Oakland | Midland |
| 31 | Jose Mejias | RHP | Durham (TB) | New York (NL) | VSL Mets |
| 32 | Corey Hamman | LHP | Indianapolis (PIT) | Detroit | Toledo |
| 33 | Clayton Hamilton | RHP | Oklahoma (TEX) | Pittsburgh | Lynchburg |
| 34 | Scott Mitchinson | RHP | Sacramento (OAK) | Philadelphia | Lakeland |
| 35 | Juan Sandoval | RHP | Nashville (MIL) | Seattle | Tacoma |
| 36 | Jaime Trejo | 3B | Oklahoma (TEX) | Atlanta | Quintana Roo |
Double-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2007 Club |
| 1 | Rafael Cruz Chavez | RHP | Altoona (PIT) | Los Angeles (AL) | Veracruz |
| 2 | J.P Martinez | RHP | Bowie (BAL) | Minnesota | Rochester |
| 3 | Kenny Fernandez | RHP | Carolina (FLA) | Philadelphia | DSL Phillies |
| 4 | Francisco Cordova | RHP | Frisco (TEX) | Los Angeles (AL) | Quintana Roo |
| 5 | Baltazar Lopez | 1B | Mobile (ARI) | Los Angeles (AL) | Chihuahua |
| 6 | Adalberto Mendez | RHP | Carolina (FLA) | Chicago (NL) | Tennessee |
