| 1 | 17 | June-Reg | Cole Hamels | | P | 18 | 12/27/1983 | 6-3 | 170 | L | L | MLB | 2006-2008 | Rancho Bernardo High School (San Diego,CA) |
| 2 | 58 | June-Reg | Zach Segovia | | P | 19 | 4/11/1983 | 6-1 | 220 | R | R | MLB | 2007-2007 | Forney High School (Forney,TX) |
| 3 | 89 | June-Reg | Kiel Fisher | | 3B | 18 | 9/29/1983 | 6-4 | 190 | L | R | A | | Poly High School (Riverside,CA) |
| 5 | 149 | June-Reg | Jake Blalock | | OF-3B | 18 | 8/6/1983 | 6-4 | 200 | R | R | AA | | Rancho Bernardo High School (San Diego,CA) |
| 6 | 179 | June-Reg | Lee Gwaltney | | P | 22 | 5/6/1980 | 6-6 | 215 | R | R | AA | | Louisiana Tech University |
| 8 | 239** | June-Reg | Steve Doetsch | | OF | 18 | 12/2/1983 | 6-2 | 185 | R | R | A+ | | Dunedin High School (Dunedin,FL) |
| 9 | 269 | June-Reg | Rob Harrand | | P | 22 | 1/11/1980 | 6-5 | 205 | R | R | A- | | San Diego State University |
| 11 | 329** | June-Reg | T.J. Beam | | P | 21 | 8/28/1980 | 6-7 | 215 | R | R | MLB | 2006-2006 | University of Mississippi |
| 13 | 389 | June-Reg | Brian Manfred | | C | 23 | 4/11/1979 | 6-2 | 215 | R | R | A | | San Diego State University |
| 17 | 509 | June-Reg | Scott Mathieson | | P | 18 | 2/27/1984 | 6-3 | 190 | R | R | MLB | 2006-2006 | Aldergrove High School (Aldergrove,BC) |
| 19 | 569 | June-Reg | Bobby Korecky | | P | 22 | 9/16/1979 | 6-0 | 180 | R | R | MLB | 2008-2008 | University of Texas-San Antonio |
| 22 | 659** | June-Reg | Brad McCann | | IF | 19 | 12/9/1982 | 6-3 | 200 | R | R | AAA | | Gulf Coast Community College |
| 26 | 779 | June-Reg | Erik Winegarden | | C | 22 | 12/5/1979 | 6-1 | 200 | L | R | A | | New Mexico State University |
| 27 | 809 | June-Reg | Brad Busbin | | P | 21 | 8/29/1980 | 6-3 | 205 | R | R | A- | | University of Central Florida |
| 28 | 839 | June-Reg | Derek Brewster | | P | 23 | 12/8/1978 | 5-11 | 220 | R | R | A- | | Louisiana Tech University |
| 29 | 869 | June-Reg | Adam Steen | | P | 22 | 6/19/1980 | 6-4 | 200 | R | R | A- | | Minnesota State University Mankato |
| 31 | 929 | June-Reg | Jeremy Isenhower | | 2B | 22 | 4/12/1980 | 5-10 | 175 | L | R | A | | Southwest Missouri State University |
| 33 | 989 | June-Reg | Jeremy Rogelstad | | P | 23 | 11/29/1978 | 6-7 | 195 | R | R | A- | | San Jose State University |
| 41 | 1229** | June-Reg | McCay Green | | P | 18 | 7/3/1983 | 6-3 | 190 | R | R | - | | Edgewater High School (Orlando,FL) |
| 45 | 1343** | June-Reg | Sam LeCure | | P | 18 | 5/4/1984 | 6-1 | 190 | R | R | AA | | Helias High School (Jefferson City,MO) |
| 46 | 1370** | June-Reg | Dusty Ryan | | C | 17 | 9/2/1984 | 6-4 | 230 | R | R | AA | | Golden Valley High School (Merced,CA) |
| 48 | 1422 | June-Reg | Dennis Winn | | | | | | | | | A | | Home School High School (Bowling Green,Ky) |