| 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 | 2 | 45 | June-Reg | Jason Taylor | Kansas City Royals | SS | A+ | 2006-2012 | H | Kellam (Virginia Beach,VA) | SF | VA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 46 | June-Reg | David Christensen | Colorado Rockies | OF | A+ | 2006-2012 | H | Douglas (Parkland,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 47 | June-Reg | Josh Butler | Tampa Bay Rays | P | MLB | 2004-2012 | C | University of San Diego | SF | CA | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 9.00 | 0 | 4 | 3 | 0 |
| 2006 | 2 | 48 | June-Reg | Mike Felix | Pittsburgh Pirates | P | A+ | 2004-2010 | C | Troy University | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 49 | June-Reg | Chris Tillman | Seattle Mariners | P | MLB | 2006-2013 | H | Fountain Valley (Fountain Valley,CA) | SF | CA | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 16 | 18 | 4.72 | 0 | 267 | 182 | 51 |
| 2006 | 2 | 50 | June-Reg | Ronnie Bourquin | Detroit Tigers | 3B | AA | 2004-2012 | C | Ohio State University | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 51 | June-Reg | Jeff Locke | Atlanta Braves | P | MLB | 2006-2013 | H | Kennett (North Conway,NH) | SF | NH | 16 | 0 | 0 | 0 | 0 | 0 | .062 | 1 | 6 | 5.82 | 0 | 51 | 39 | 10 |
| 2006 | 2 | 52 | June-Reg | Sean Watson | Cincinnati Reds | P | AAA | 2004-2011 | C | University of Tennessee | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 53 | June-Reg | Chad Huffman | San Diego Padres | 2B | MLB | 2004-2013 | C | Texas Christian University | SF | TX | 18 | 0 | 0 | 0 | 2 | 0 | .167 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 54 | June-Reg | Brad Furnish | St. Louis Cardinals | P | AA | 2004-2012 | C | Texas Christian University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 55 | June-Reg | Brett Anderson | Arizona Diamondbacks | P | MLB | 2007-2013 | H | Stillwater (Stillwater,OK) | SF | OK | 4 | 0 | 0 | 0 | 0 | 0 | .000 | 25 | 25 | 3.57 | 0 | 406 | 311 | 68 |
| 2006 | 2 | 56 | June-Reg | Steve Wright | Cleveland Indians | P | MLB | 2004-2013 | C | University of Hawaii | SF | HI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 57 | June-Reg | Josh Rodriguez | Cleveland Indians | 2B | MLB | 2004-2013 | C | Rice University | SF | TX | 12 | 0 | 0 | 0 | 1 | 0 | .083 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 58 | June-Reg | Ryan Adams | Baltimore Orioles | 3B | MLB | 2006-2012 | H | Jesuit (New Orleans,LA) | SF | LA | 89 | 4 | 0 | 0 | 7 | 0 | .281 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 59 | June-Reg | Sean Black ** | Washington Nationals | P | A+ | 2007-2013 | H | Lenape (Medford,NJ) | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 60 | June-Reg | Brent Brewer | Milwaukee Brewers | SS | AA | 2006-2010 | H | Sandy Creek (Tyrone,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 61 | June-Reg | Wade LeBlanc | San Diego Padres | P | MLB | 2004-2013 | C | University of Alabama | SF | AL | 99 | 1 | 0 | 0 | 2 | 0 | .263 | 19 | 27 | 4.38 | 0 | 362 | 248 | 61 |
| 2006 | 2 | 62 | June-Reg | Kevin Mulvey | New York Mets | P | MLB | 2004-2012 | C | Villanova University | SF | PA | 7 | 0 | 0 | 0 | 0 | 0 | .143 | 0 | 3 | 7.90 | 0 | 27 | 19 | 4 |
| 2006 | 2 | 63 | June-Reg | Thomas Hickman | Florida Marlins | CF | A+ | 2006-2010 | H | Pepperell (Rome,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 64 | June-Reg | Joe Benson | Minnesota Twins | LF | MLB | 2006-2013 | H | Catholic Academy (Joliet,IL) | SF | IL | 71 | 6 | 1 | 0 | 2 | 2 | .239 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 65 | June-Reg | Drew Carpenter | Philadelphia Phillies | P | MLB | 2006-2013 | C | Long Beach State University | SF | CA | 4 | 0 | 0 | 0 | 0 | 0 | .000 | 1 | 1 | 7.56 | 0 | 33 | 33 | 1 |
| 2006 | 2 | 66 | June-Reg | Trevor Cahill | Oakland Athletics | P | MLB | 2006-2013 | H | Vista (Vista,CA) | SF | CA | 77 | 0 | 0 | 0 | 4 | 0 | .117 | 53 | 47 | 3.87 | 0 | 783 | 511 | 128 |
| 2006 | 2 | 67 | June-Reg | Sergio Perez | Houston Astros | P | AAA | 2006-2013 | C | University of Tampa | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 68 | June-Reg | Dustin Evans | Atlanta Braves | P | AA | 2004-2008 | C | Georgia Southern University | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 69 | June-Reg | Wes Hodges | Cleveland Indians | 3B | AAA | 2004-2012 | C | Georgia Tech | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 70 | June-Reg | Stephen Englund | Washington Nationals | OF | A | 2006-2009 | H | Bellevue (Bellevue,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 71 | June-Reg | Justin Masterson | Boston Red Sox | P | MLB | 2006-2013 | C | San Diego State University | SF | CA | 17 | 0 | 0 | 0 | 0 | 0 | .118 | 39 | 53 | 4.17 | 0 | 820 | 644 | 121 |
| 2006 | 2 | 72 | June-Reg | Chase Fontaine | Atlanta Braves | SS | A+ | 2006-2012 | C | Daytona State College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 73 | June-Reg | Matt Long | Chicago White Sox | P | AAA | 2003-2011 | C | Miami University | SF | OH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 74 | June-Reg | Jon Jay | St. Louis Cardinals | OF | MLB | 2004-2013 | C | University of Miami | SF | FL | 1185 | 65 | 8 | 18 | 104 | 27 | .300 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 75 | June-Reg | Matt McBride | Cleveland Indians | C | MLB | 2004-2013 | C | Lehigh University | SF | PA | 78 | 2 | 0 | 2 | 11 | 0 | .205 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 2 | 76 | June-Reg | Mark Hamilton | St. Louis Cardinals | 1B | MLB | 2004-2013 | C | Tulane University | SF | LA | 61 | 3 | 0 | 0 | 4 | 0 | .197 | -- | -- | -- | -- | -- | -- | -- |