| 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 |
| 2006 | 3 | 77 | June-Reg | Blake Wood | Kansas City Royals | P | MLB | 2004-2013 | C | Georgia Tech | SF | GA | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 6 | 6 | 4.30 | 1 | 119 | 93 | 0 |
| 2006 | 3 | 78 | June-Reg | Keith Weiser | Colorado Rockies | P | AAA | 2004-2012 | C | Miami University | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 79 | June-Reg | Nick Fuller ** | Tampa Bay Rays | P | - | H | Kell (Marietta,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 3 | 80 | June-Reg | Shelby Ford | Pittsburgh Pirates | 2B | AAA | 2004-2012 | C | Oklahoma State University | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 81 | June-Reg | Tony Butler | Seattle Mariners | P | A | 2006-2012 | H | Oak Creek (Milwaukee,WI) | SF | WI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 82 | June-Reg | Brennan Boesch | Detroit Tigers | CF | MLB | 2004-2013 | C | University of California | SF | CA | 1362 | 73 | 6 | 42 | 175 | 18 | .259 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 83 | June-Reg | Aaron Bates | Boston Red Sox | 1B | MLB | 2003-2012 | C | North Carolina State University | SF | NC | 11 | 2 | 0 | 0 | 2 | 0 | .364 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 84 | June-Reg | Chris Valaika | Cincinnati Reds | SS | MLB | 2004-2013 | C | University of California-Santa Barbara | SF | CA | 63 | 2 | 1 | 1 | 2 | 0 | .270 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 85 | June-Reg | Zach Britton | Baltimore Orioles | P | MLB | 2006-2013 | H | Weatherford (Weatherford,TX) | SF | TX | 8 | 1 | 0 | 1 | 2 | 0 | .625 | 16 | 14 | 4.74 | 0 | 215 | 150 | 39 |
| 2006 | 3 | 86 | June-Reg | Dallas Buck | Arizona Diamondbacks | P | AA | 2004-2011 | C | Oregon State University | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 87 | June-Reg | Cyle Hankerd | Arizona Diamondbacks | LF | AAA | 2004-2012 | C | USC | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 88 | June-Reg | Chad Tracy | Texas Rangers | C | AAA | 2004-2012 | C | Pepperdine University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 89 | June-Reg | Clayton Tanner | San Francisco Giants | P | AAA | 2006-2012 | H | De La Salle (Concord,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 90 | June-Reg | Torre Langley | Florida Marlins | C | AA | 2006-2011 | H | Alexander (Douglasville,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 91 | June-Reg | Stephen King | Washington Nationals | SS | AA | 2007-2012 | H | Winter Park (Winter Park,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 92 | June-Reg | Cole Gillespie | Milwaukee Brewers | LF | MLB | 2004-2013 | C | Oregon State University | SF | OR | 110 | 8 | 0 | 3 | 16 | 1 | .236 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 93 | June-Reg | Cedric Hunter | San Diego Padres | CF | MLB | 2006-2013 | H | Martin Luther King (Lithonia,GA) | SF | GA | 4 | 0 | 0 | 0 | 0 | 0 | .250 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 94 | June-Reg | Joe Smith | New York Mets | P | MLB | 2004-2013 | C | Wright State University | SF | OH | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 21 | 14 | 3.11 | 0 | 316 | 257 | 0 |
| 2006 | 3 | 95 | June-Reg | Scott Cousins | Florida Marlins | LF | MLB | 2004-2013 | C | University of San Francisco | SF | CA | 175 | 7 | 3 | 2 | 9 | 2 | .183 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 96 | June-Reg | Tyler Robertson | Minnesota Twins | P | MLB | 2006-2013 | H | Bella Vista (Fair Oaks,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | 2 | 2 | 5.40 | 0 | 25 | 26 | 0 |
| 2006 | 3 | 97 | June-Reg | Jason Donald | Philadelphia Phillies | SS | MLB | 2004-2013 | C | University of Arizona | SF | AZ | 552 | 27 | 5 | 7 | 43 | 12 | .257 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 98 | June-Reg | Matthew Sulentic | Oakland Athletics | OF | AA | 2006-2011 | H | Hillcrest (Dallas,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 99 | June-Reg | Nick Moresi | Houston Astros | CF | AA | 2004-2010 | C | Fresno State University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 100 | June-Reg | Chad Rodgers | Atlanta Braves | P | A+ | 2006-2013 | H | Walsh Jesuit (Cuyahoga Falls,OH) | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 101 | June-Reg | Adam Davis | Cleveland Indians | SS | AA | 2004-2010 | C | University of Florida | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 102 | June-Reg | Russell Moldenhauer ** | Los Angeles Angels | OF | A | 2007-2012 | H | Boerne (Boerne,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 103 | June-Reg | Bryce Cox | Boston Red Sox | P | AA | 2005-2010 | C | Rice University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 104 | June-Reg | Zach McAllister | New York Yankees | P | MLB | 2006-2013 | H | Illinois Valley Central (Peoria,IL) | SF | IL | -- | -- | -- | -- | -- | -- | -- | 6 | 9 | 4.47 | 0 | 143 | 124 | 26 |
| 2006 | 3 | 105 | June-Reg | Justin Edwards | Chicago White Sox | P | AA | 2006-2011 | H | Olympia (Orlando,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 106 | June-Reg | Gary Daley | St. Louis Cardinals | P | AAA | 2004-2013 | C | Cal Poly | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |