| 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 | 1 | 1 | June-Reg | Luke Hochevar | Kansas City Royals | P | MLB | 2003-2013 | H | Fowler (Fowler,CO) | SF | 16 | 0 | 0 | 0 | 0 | 0 | .062 | 38 | 59 | 5.39 | 0 | 771 | 531 | 128 | |
| 2006 | 1 | 2 | June-Reg | Greg Reynolds | Colorado Rockies | P | MLB | 2004-2013 | C | Stanford University | SF | CA | 23 | 2 | 0 | 0 | 0 | 0 | .174 | 5 | 8 | 7.47 | 0 | 94 | 40 | 16 |
| 2006 | 1 | 3 | June-Reg | Evan Longoria | Tampa Bay Rays | 3B | MLB | 2004-2013 | C | Long Beach State University | SF | CA | 2362 | 161 | 8 | 130 | 456 | 36 | .276 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 4 | June-Reg | Brad Lincoln | Pittsburgh Pirates | P | MLB | 2004-2013 | C | University of Houston | SF | TX | 37 | 1 | 0 | 0 | 4 | 0 | .243 | 8 | 9 | 4.78 | 1 | 188 | 142 | 22 |
| 2006 | 1 | 5 | June-Reg | Brandon Morrow | Seattle Mariners | P | MLB | 2004-2013 | C | University of California | SF | CA | 12 | 0 | 0 | 0 | 0 | 0 | .000 | 39 | 37 | 4.10 | 16 | 648 | 693 | 92 |
| 2006 | 1 | 6 | June-Reg | Andrew Miller | Detroit Tigers | P | MLB | 2004-2013 | C | University of North Carolina | SF | NC | 72 | 0 | 0 | 0 | 3 | 0 | .056 | 24 | 31 | 5.54 | 0 | 400 | 339 | 66 |
| 2006 | 1 | 7 | June-Reg | Clayton Kershaw | Los Angeles Dodgers | P | MLB | 2006-2013 | H | Highland Park (Dallas,TX) | SF | TX | 261 | 1 | 0 | 0 | 9 | 0 | .146 | 61 | 37 | 2.79 | 0 | 944 | 974 | 149 |
| 2006 | 1 | 8 | June-Reg | Drew Stubbs | Cincinnati Reds | CF | MLB | 2004-2013 | C | University of Texas | SF | TX | 1791 | 59 | 12 | 59 | 178 | 110 | .241 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 9 | June-Reg | Billy Rowell | Baltimore Orioles | 3B | AA | 2006-2011 | H | Bishop Eustace Preparator (Pennsauken,NJ) | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 10 | June-Reg | Tim Lincecum | San Francisco Giants | P | MLB | 2004-2013 | C | University of Washington | SF | WA | 352 | 3 | 1 | 0 | 17 | 0 | .116 | 79 | 56 | 3.31 | 0 | 1214 | 1317 | 188 |
| 2006 | 1 | 11 | June-Reg | Max Scherzer | Arizona Diamondbacks | P | MLB | 2004-2013 | C | University of Missouri | SF | MO | 74 | 2 | 0 | 0 | 3 | 0 | .162 | 52 | 42 | 3.88 | 0 | 805 | 829 | 133 |
| 2006 | 1 | 12 | June-Reg | Kasey Kiker | Texas Rangers | P | AA | 2006-2012 | H | Russell County (Seale,AL) | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 13 | June-Reg | Tyler Colvin | Chicago Cubs | LF | MLB | 2004-2013 | C | Clemson University | SF | SC | 1001 | 53 | 18 | 44 | 150 | 13 | .247 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 14 | June-Reg | Travis Snider | Toronto Blue Jays | RF | MLB | 2006-2013 | H | Jackson (Mill Creek,WA) | SF | WA | 963 | 61 | 2 | 32 | 121 | 18 | .248 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 15 | June-Reg | Chris Marrero | Washington Nationals | OF | MLB | 2006-2013 | H | Monsignor Pace (Miami,FL) | SF | FL | 109 | 5 | 0 | 0 | 10 | 0 | .248 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 16 | June-Reg | Jeremy Jeffress | Milwaukee Brewers | P | MLB | 2006-2013 | H | Halifax County (South Boston,VA) | SF | VA | -- | -- | -- | -- | -- | -- | -- | 2 | 1 | 4.89 | 1 | 39 | 34 | 0 |
| 2006 | 1 | 17 | June-Reg | Matt Antonelli | San Diego Padres | 3B | MLB | 2004-2013 | C | Wake Forest University | SF | NC | 57 | 2 | 0 | 1 | 3 | 0 | .193 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 18 | June-Reg | Kyle Drabek | Philadelphia Phillies | P | MLB | 2006-2012 | H | The Woodlands (The Woodlands,TX) | SF | TX | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 8 | 15 | 5.34 | 0 | 167 | 110 | 30 |
| 2006 | 1 | 19 | June-Reg | Brett Sinkbeil | Florida Marlins | P | MLB | 2004-2011 | C | Missouri State University | SF | MO | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 13.50 | 0 | 2 | 1 | 0 |
| 2006 | 1 | 20 | June-Reg | Chris Parmelee | Minnesota Twins | RF | MLB | 2006-2013 | H | Chino Hills (Chino Hills,CA) | SF | CA | 268 | 16 | 2 | 9 | 34 | 0 | .265 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 21 | June-Reg | Ian Kennedy | New York Yankees | P | MLB | 2004-2013 | C | USC | SF | CA | 166 | 4 | 1 | 0 | 12 | 0 | .139 | 46 | 30 | 3.76 | 0 | 684 | 596 | 110 |
| 2006 | 1 | 22 | June-Reg | Colton Willems | Washington Nationals | P | A+ | 2006-2010 | H | Carroll (Fort Pierce,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 23 | June-Reg | Maxwell Sapp | Houston Astros | C | A | 2006-2008 | H | Bishop Moore (Orlando,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 24 | June-Reg | Cody Johnson | Atlanta Braves | OF | AAA | 2006-2013 | H | Mosley (Panama City,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 25 | June-Reg | Hank Conger | Los Angeles Angels | C | MLB | 2006-2013 | H | Huntington Beach (Huntington Beach,CA) | SF | CA | 224 | 9 | 1 | 6 | 25 | 0 | .201 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 26 | June-Reg | Bryan Morris | Los Angeles Dodgers | P | MLB | 2006-2013 | C | Motlow State Community College | SF | TN | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 1.80 | 0 | 5 | 6 | 0 |
| 2006 | 1 | 27 | June-Reg | Jason Place | Boston Red Sox | CF | AA | 2006-2011 | H | Wren (Piedmont,SC) | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 28 | June-Reg | Daniel Bard | Boston Red Sox | P | MLB | 2004-2013 | C | University of North Carolina | SF | NC | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 10 | 19 | 3.65 | 5 | 256 | 251 | 10 |
| 2006 | 1 | 29 | June-Reg | Kyle McCulloch | Chicago White Sox | P | AAA | 2004-2011 | C | University of Texas | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 30 | June-Reg | Adam Ottavino | St. Louis Cardinals | P | MLB | 2004-2013 | C | Northeastern University | SF | MA | 15 | 0 | 0 | 0 | 0 | 0 | .067 | 5 | 3 | 5.42 | 0 | 101 | 93 | 3 |
| 2006 | 1 | 31 | June-Reg | Preston Mattingly | Los Angeles Dodgers | SS | A+ | 2006-2011 | H | Evansville Central (Evansville,IN) | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 32 | June-Reg | Pedro Beato | Baltimore Orioles | P | MLB | 2006-2013 | C | St. Petersburg College | SF | FL | -- | -- | -- | -- | -- | -- | -- | 3 | 1 | 4.67 | 0 | 79 | 51 | 0 |
| 2006 | 1 | 33 | June-Reg | Emmanuel Burriss | San Francisco Giants | SS | MLB | 2004-2013 | C | Kent State University | SF | OH | 720 | 14 | 1 | 1 | 42 | 40 | .243 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 34 | June-Reg | Brooks Brown | Arizona Diamondbacks | P | AAA | 2004-2013 | C | University of Georgia | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 35 | June-Reg | Kyler Burke | San Diego Padres | RF | A+ | 2006-2013 | H | Ooltewah (Ooltewah,TN) | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 36 | June-Reg | Chris Coghlan | Florida Marlins | 3B | MLB | 2004-2013 | C | University of Mississippi | SF | MS | 1224 | 72 | 10 | 20 | 107 | 25 | .272 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 37 | June-Reg | Adrian Cardenas | Philadelphia Phillies | SS | MLB | 2006-2012 | H | Monsignor Pace (Miami,FL) | SF | FL | 60 | 6 | 0 | 0 | 2 | 0 | .183 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 38 | June-Reg | Cory Rasmus | Atlanta Braves | P | MLB | 2006-2013 | H | Russell County (Seale,AL) | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 39 | June-Reg | David Huff | Cleveland Indians | P | MLB | 2004-2013 | C | UCLA | SF | CA | 4 | 0 | 0 | 0 | 0 | 0 | .000 | 18 | 26 | 5.30 | 0 | 285 | 157 | 52 |
| 2006 | 1 | 40 | June-Reg | Kris Johnson | Boston Red Sox | P | AAA | 2004-2013 | C | Wichita State University | SF | KS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 41 | June-Reg | Joba Chamberlain | New York Yankees | P | MLB | 2005-2013 | C | University of Nebraska | SF | NE | 5 | 0 | 0 | 0 | 0 | 0 | .000 | 21 | 13 | 3.73 | 4 | 403 | 408 | 43 |
| 2006 | 1 | 42 | June-Reg | Chris Perez | St. Louis Cardinals | P | MLB | 2004-2013 | C | University of Miami | SF | FL | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 10 | 18 | 3.23 | 107 | 279 | 269 | 0 |
| 2006 | 1 | 43 | June-Reg | Steven Evarts | Atlanta Braves | P | A | 2006-2012 | H | Robinson (Tampa,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 1 | 44 | June-Reg | Caleb Clay | Boston Red Sox | P | AA | 2007-2013 | H | Cullman (Cullman,AL) | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |