| Year | Rnd | Ovl | Phase | Player | Drafting Team | Pos | HiLvl | Played | Src | Drafted From | SF | State | AB | 2B | 3B | HR | RBI | SB | BAVG | W | L | ERA | SV | IP | SO | GS |
| 2003 | 2 | 38 | June-Reg | James Houser | Tampa Bay Rays | P | MLB | 2003-2012 | H | Sarasota (Sarasota,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 20.25 | 0 | 1 | 1 | 0 |
| 2003 | 2 | 39 | June-Reg | Tony Gwynn | Milwaukee Brewers | OF | MLB | 2001-2013 | C | San Diego State University | SF | CA | 1495 | 46 | 22 | 7 | 95 | 77 | .244 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 40 | June-Reg | Jay Sborz | Detroit Tigers | P | MLB | 2003-2010 | H | Langley (McLean,VA) | SF | VA | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 67.50 | 0 | 1 | 1 | 0 |
| 2003 | 2 | 41 | June-Reg | Daniel Moore | San Diego Padres | P | A | 2001-2004 | C | University of North Carolina | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 42 | June-Reg | Shane Costa | Kansas City Royals | OF | MLB | 2001-2012 | C | Cal State Fullerton | SF | CA | 421 | 28 | 2 | 5 | 42 | 2 | .254 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 43 | June-Reg | Jo-Jo Reyes | Atlanta Braves | P | MLB | 2003-2012 | H | Riverside Poly (Riverside,CA) | SF | CA | 63 | 2 | 0 | 0 | 2 | 0 | .143 | 12 | 26 | 6.05 | 0 | 335 | 215 | 62 |
| 2003 | 2 | 44 | June-Reg | Brian Finch | Baltimore Orioles | P | AA | 2001-2008 | C | Texas A&M University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 45 | June-Reg | Tom Gorzelanny | Pittsburgh Pirates | P | MLB | 2002-2013 | C | Triton College | SF | IL | 199 | 0 | 0 | 0 | 13 | 0 | .095 | 44 | 45 | 4.41 | 2 | 735 | 568 | 111 |
| 2003 | 2 | 46 | June-Reg | Vince Sinisi | Texas Rangers | 1B | AAA | 2002-2009 | C | Rice University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 47 | June-Reg | Scott Beerer | Colorado Rockies | P | AAA | 2003-2012 | C | Texas A&M University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 48 | June-Reg | Javier Herrera | Cleveland Indians | C | AAA | 2001-2008 | C | University of Tennessee | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 49 | June-Reg | Abe Alvarez | Boston Red Sox | P | MLB | 2001-2008 | C | Long Beach State University | SF | CA | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 0 | 1 | 11.32 | 0 | 10 | 5 | 1 |
| 2003 | 2 | 50 | June-Reg | Josh Banks | Toronto Blue Jays | P | MLB | 2001-2011 | C | Florida International University | SF | FL | 27 | 0 | 0 | 0 | 0 | 0 | .111 | 4 | 8 | 5.66 | 0 | 119 | 55 | 19 |
| 2003 | 2 | 51 | June-Reg | Thomas Pauly | Cincinnati Reds | P | A+ | 2001-2007 | C | Princeton University | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 52 | June-Reg | Ryan Sweeney | Chicago White Sox | OF | MLB | 2003-2013 | H | Xavier (Cedar Rapids,IA) | SF | IA | 1719 | 102 | 12 | 14 | 185 | 17 | .280 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 53 | June-Reg | Logan Kensing | Florida Marlins | P | MLB | 2002-2013 | C | Texas A&M University | SF | TX | 8 | 0 | 0 | 0 | 0 | 0 | .000 | 8 | 9 | 5.81 | 2 | 161 | 143 | 3 |
| 2003 | 2 | 54 | June-Reg | Mickey Hall | Boston Red Sox | OF | AAA | 2003-2009 | H | Walton (Marietta,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 55 | June-Reg | Todd Jennings | San Francisco Giants | C | AAA | 2001-2012 | C | Long Beach State University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 56 | June-Reg | Jeff Flaig | Seattle Mariners | 3B | A+ | 2004-2007 | H | El Dorado (Placentia,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 57 | June-Reg | Jerry Owens | Montreal Expos | OF | MLB | 2003-2009 | C | Master's College, The | SF | CA | 393 | 10 | 2 | 1 | 18 | 36 | .262 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 58 | June-Reg | Scott Baker | Minnesota Twins | P | MLB | 2001-2012 | C | Oklahoma State University | SF | OK | 25 | 1 | 0 | 0 | 0 | 0 | .120 | 63 | 48 | 4.15 | 0 | 958 | 770 | 159 |
| 2003 | 2 | 59 | June-Reg | Jason Hirsh | Houston Astros | P | MLB | 2003-2010 | C | California Lutheran University | SF | CA | 50 | 0 | 0 | 0 | 2 | 0 | .060 | 8 | 11 | 5.32 | 0 | 166 | 110 | 29 |
| 2003 | 2 | 60 | June-Reg | Anthony Whittington | Anaheim Angels | P | RK | 2003-2005 | H | Buffalo (Buffalo,WV) | SF | WV | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 61 | June-Reg | Chuck Tiffany | Los Angeles Dodgers | P | AA | 2003-2011 | H | Charter Oak (Covina,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 62 | June-Reg | Andre Ethier | Oakland Athletics | OF | MLB | 2002-2013 | C | Arizona State University | SF | AZ | 3524 | 231 | 19 | 129 | 535 | 21 | .290 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 63 | June-Reg | Nate Schierholtz | San Francisco Giants | 3B | MLB | 2003-2013 | C | Chabot College | SF | CA | 1275 | 75 | 15 | 24 | 123 | 20 | .270 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 64 | June-Reg | Estee Harris | New York Yankees | OF | A+ | 2003-2011 | H | Central Islip (Central Islip,NY) | SF | NY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 65 | June-Reg | Stuart Pomeranz | St. Louis Cardinals | P | MLB | 2003-2012 | H | Houston (Germantown,TN) | SF | TN | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 3.00 | 0 | 6 | 3 | 0 |
| 2003 | 2 | 66 | June-Reg | Jamie D'Antona | Arizona Diamondbacks | 3B | MLB | 2001-2010 | C | Wake Forest University | SF | NC | 17 | 0 | 0 | 0 | 1 | 0 | .176 | -- | -- | -- | -- | -- | -- | -- |
| 2003 | 2 | 67 | June-Reg | Paul Bacot | Atlanta Braves | P | A | 2003-2005 | H | Lakeside (Atlanta,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |