| 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 |
| 2004 | 2 | 42 | June-Reg | Brett Smith | New York Yankees | P | AA | 2002-2010 | C | University of California-Irvine | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 43 | June-Reg | Eric Beattie | Detroit Tigers | P | A | 2002-2007 | C | University of Tampa | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 44 | June-Reg | Matt Durkin | New York Mets | P | A | 2002-2012 | C | San Jose State University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 45 | June-Reg | Reid Brignac | Tampa Bay Rays | SS | MLB | 2004-2013 | H | St. Amant (St. Amant,LA) | SF | LA | 671 | 25 | 3 | 10 | 67 | 8 | .227 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 46 | June-Reg | Yovani Gallardo | Milwaukee Brewers | P | MLB | 2004-2013 | H | Trimble Technical (Fort Worth,TX) | SF | TX | 305 | 17 | 0 | 10 | 37 | 0 | .207 | 69 | 43 | 3.63 | 0 | 916 | 936 | 148 |
| 2004 | 2 | 47 | June-Reg | Justin Hoyman | Cleveland Indians | P | A | 2003-2005 | C | University of Florida | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 48 | June-Reg | B.J. Szymanski | Cincinnati Reds | OF | AAA | 2003-2008 | C | Princeton University | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 49 | June-Reg | Michael Rogers | Oakland Athletics | P | AA | 2002-2009 | C | North Carolina State University | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 50 | June-Reg | Seth Smith | Colorado Rockies | OF | MLB | 2002-2013 | C | University of Mississippi | SF | MS | 1668 | 101 | 21 | 65 | 233 | 19 | .267 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 51 | June-Reg | K.C. Herren | Texas Rangers | OF | A+ | 2004-2009 | H | Auburn (Auburn,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 52 | June-Reg | Brian Bixler | Pittsburgh Pirates | SS | MLB | 2002-2013 | C | Eastern Michigan University | SF | MI | 323 | 14 | 3 | 2 | 14 | 9 | .189 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 53 | June-Reg | Wes Whisler | Chicago White Sox | P | MLB | 2002-2013 | C | UCLA | SF | CA | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 13.50 | 0 | 1 | 2 | 0 |
| 2004 | 2 | 54 | June-Reg | Erick San Pedro | Montreal Expos | C | AAA | 2002-2008 | C | University of Miami | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 55 | June-Reg | Billy Buckner | Kansas City Royals | P | MLB | 2004-2012 | C | University of South Carolina | SF | SC | 26 | 2 | 0 | 0 | 6 | 0 | .231 | 6 | 11 | 6.25 | 0 | 138 | 103 | 21 |
| 2004 | 2 | 56 | June-Reg | Jon Zeringue | Arizona Diamondbacks | OF | AA | 2002-2008 | C | Louisiana State University | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 57 | June-Reg | Curtis Thigpen | Toronto Blue Jays | C | MLB | 2002-2008 | C | University of Texas | SF | TX | 118 | 5 | 0 | 1 | 12 | 2 | .229 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 58 | June-Reg | Blake Johnson | Los Angeles Dodgers | P | AAA | 2004-2013 | H | Parkview Baptist (Baton Rouge,LA) | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 59 | June-Reg | Donny Lucy | Chicago White Sox | C | MLB | 2002-2011 | C | Stanford University | SF | CA | 40 | 4 | 0 | 1 | 3 | 1 | .250 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 60 | June-Reg | Mike Ferris | St. Louis Cardinals | 1B | AAA | 2002-2007 | C | Miami University | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 61 | June-Reg | Anthony Swarzak | Minnesota Twins | P | MLB | 2004-2013 | H | Nova (Davie,FL) | SF | FL | 4 | 0 | 0 | 0 | 0 | 0 | .000 | 10 | 20 | 5.03 | 0 | 258 | 151 | 28 |
| 2004 | 2 | 62 | June-Reg | Jason Jaramillo | Philadelphia Phillies | C | MLB | 2002-2013 | C | Oklahoma State University | SF | OK | 336 | 19 | 0 | 4 | 38 | 2 | .235 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 63 | June-Reg | Erik Cordier | Kansas City Royals | P | AAA | 2004-2013 | H | Southern Door (Brussels,WI) | SF | WI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 64 | June-Reg | Hunter Pence | Houston Astros | OF | MLB | 2003-2013 | C | University of Texas-Arlington | SF | TX | 3473 | 183 | 30 | 138 | 516 | 67 | .285 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 65 | June-Reg | Dustin Pedroia | Boston Red Sox | SS | MLB | 2002-2013 | C | Arizona State University | SF | AZ | 3388 | 245 | 11 | 90 | 409 | 102 | .303 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 66 | June-Reg | Grant Johnson | Chicago Cubs | P | AA | 2002-2009 | C | University of Notre Dame | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 67 | June-Reg | Kurt Suzuki | Oakland Athletics | C | MLB | 2002-2013 | C | Cal State Fullerton | SF | CA | 2676 | 139 | 4 | 62 | 327 | 17 | .255 | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 68 | June-Reg | Jason Vargas | Florida Marlins | P | MLB | 2002-2013 | C | Long Beach State University | SF | CA | 61 | 3 | 0 | 0 | 4 | 0 | .262 | 42 | 50 | 4.35 | 0 | 830 | 530 | 130 |
| 2004 | 2 | 69 | June-Reg | Ray Liotta | Chicago White Sox | P | AAA | 2002-2009 | C | Gulf Coast State College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 70 | June-Reg | Eddy Martinez-Estevez | San Francisco Giants | OF | AAA | 2004-2012 | C | Florida State University | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2004 | 2 | 71 | June-Reg | Eric Campbell | Atlanta Braves | 3B | AA | 2004-2012 | H | Gibson Southern (Fort Branch,IN) | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |