| 1 | 17 | June-Reg | Cole Hamels | P | 18 | 6-3 | 170 | L | L | MLB | 2006-2009 | Rancho Bernardo (San Diego,CA) | $2,000,000 |
| 2 | 58 | June-Reg | Zach Segovia | P | 19 | 6-1 | 220 | R | R | MLB | 2007-2009 | Forney (Forney,TX) | |
| 3 | 89 | June-Reg | Kiel Fisher | 3B | 18 | 6-4 | 190 | L | R | A | | Poly (Riverside,CA) | |
| 4 | 119 | June-Reg | Nick Bourgeois | P | 21 | 6-4 | 210 | L | L | AA | | Tulane University | |
| 5 | 149 | June-Reg | Jake Blalock | OF-3B | 18 | 6-4 | 200 | R | R | AA | | Rancho Bernardo (San Diego,CA) | |
| 6 | 179 | June-Reg | Lee Gwaltney | P | 22 | 6-6 | 215 | R | R | AAA | | Louisiana Tech University | |
| 7 | 209 | June-Reg | Robby Read | P | 20 | 6-2 | 195 | R | R | A+ | | Florida State University | |
| 8 | 239** | June-Reg | Steve Doetsch | OF | 18 | 6-2 | 185 | R | R | A+ | | Dunedin (Dunedin,FL) | |
| 9 | 269 | June-Reg | Rob Harrand | P | 22 | 6-5 | 205 | R | R | A- | | San Diego State University | |
| 10 | 299 | June-Reg | Ryan Barthelemy | IF | 22 | 6-3 | 225 | L | R | AA | | Florida State University | |
| 11 | 329** | June-Reg | T.J. Beam | P | 21 | 6-7 | 215 | R | R | MLB | 2006-2008 | University of Mississippi | |
| 12 | 359 | June-Reg | Trent Pratt | C | 22 | 6-2 | 208 | R | R | AA | - | Auburn University | |
| 13 | 389 | June-Reg | Brian Manfred | C | 23 | 6-2 | 215 | R | R | A | | San Diego State University | |
| 14 | 419 | June-Reg | Darin Naatjes | P | 21 | 6-9 | 240 | L | R | A- | | Stanford University | |
| 15 | 449 | June-Reg | Victor Menocal | SS | 22 | 6-4 | 215 | R | R | A | | Georgia Tech | |
| 16 | 479 | June-Reg | Omar Bramasco | IF | 20 | 6-0 | 180 | R | R | AAA | | Long Beach City College | |
| 17 | 509 | June-Reg | Scott Mathieson | P | 18 | 6-3 | 190 | R | R | MLB | 2006-2006 | Aldergrove (Aldergrove,BC) | |
| 18 | 539 | June-Reg | Chad Oliva | OF | 21 | 6-0 | 215 | R | R | A | | Jacksonville University | |
| 19 | 569 | June-Reg | Bobby Korecky | P | 22 | 6-0 | 180 | R | R | MLB | 2008-2009 | University of Texas-San Antonio | |
| 20 | 599 | June-Reg | Karl Nonemaker | OF | 22 | 6-0 | 190 | L | L | AA | | Vanderbilt University | |
| 21 | 629** | June-Reg | Brett Mcmillan | | 18 | 6-5 | 225 | L | R | A+ | | Ponderosa (Shingle Springs,CA) | |
| 22 | 659** | June-Reg | Brad McCann | IF | 19 | 6-3 | 200 | R | R | AA | | Gulf Coast Community College | |
| 23 | 689 | June-Reg | Jason Fletcher | P | | | 0 | | | - | | Indian River State College | |
| 24 | 719 | June-Reg | James Bryant | P | | | 0 | | | - | | Elon University | |
| 25 | 749 | June-Reg | Zach Minor | P | 22 | 6-6 | 215 | R | R | A | | Fresno State University | |
| 26 | 779 | June-Reg | Erik Winegarden | C | 22 | 6-1 | 200 | L | R | A | | New Mexico State University | |
| 27 | 809 | June-Reg | Brad Busbin | P | 21 | 6-3 | 205 | R | R | A- | | University of Central Florida | |
| 28 | 839 | June-Reg | Derek Brewster | P | 23 | 5-11 | 220 | R | R | A- | | Louisiana Tech University | |
| 29 | 869 | June-Reg | Adam Steen | P | 22 | 6-4 | 200 | R | R | A- | | Minnesota State University-Mankato | |
| 30 | 899 | June-Reg | Ryan Wardinsky | 2B | 22 | 6-1 | 180 | B | R | A+ | | Texas A&M University | |
| 31 | 929 | June-Reg | Jeremy Isenhower | 2B | 22 | 5-10 | 175 | L | R | A | | Missouri State University | |
| 32 | 959 | June-Reg | Rob Cafiero | IF | 22 | 6-4 | 235 | R | R | A- | | Villanova University | |
| 33 | 989 | June-Reg | Jeremy Rogelstad | P | 23 | 6-7 | 195 | R | R | A- | | San Jose State University | |
| 34 | 1019 | June-Reg | Beau Richardson | P | 22 | 6-2 | 205 | L | L | A+ | | Tulane University | |
| 35 | 1049 | June-Reg | Josh Paddock | P | 21 | 6-2 | 200 | R | R | A+ | | Aurora University | |
| 36 | 1079 | June-Reg | Keahi Rawlins | | | | | | | College | | Molokai (Hoolehua,HI) | |
| 37 | 1109 | June-Reg | Tim Gradoville | C | 22 | 6-3 | 190 | R | R | AAA | | Creighton University | |
| 38 | 1139 | June-Reg | Corey Carter | CF | | | 0 | | | - | | West Point (West Point,MS) | |
| 39 | 1169 | June-Reg | Daniel Lewis | P | | | 0 | | | - | | Folsom (Folsom,TX) | |
| 40 | 1199 | June-Reg | Brandon Joseph | OF | | | 0 | | | - | | Dimond (Anchorage,AK) | |
| 41 | 1229** | June-Reg | McCay Green | P | 18 | 6-3 | 190 | R | R | - | | Edgewater (Orlando,FL) | |
| 42 | 1259 | June-Reg | Clay Dirks | P | 17 | 6-4 | 235 | L | L | College | | Hernando (Hernando,MS) | |
| 43 | 1288 | June-Reg | Byron Cragg | P | | | 0 | | | - | | Galena (Reno,NV) | |
| 44 | 1316 | June-Reg | Jacob Habsieger | P | | | 0 | | | College | | Festus (Festus,MO) | |
| 45 | 1343** | June-Reg | Sam LeCure | P | 18 | 6-1 | 190 | R | R | AAA | | Helias (Jefferson City,MO) | |
| 46 | 1370** | June-Reg | Dusty Ryan | C | 17 | 6-4 | 230 | R | R | MLB | 2008-2009 | Golden Valley (Merced,CA) | |
| 47 | 1396 | June-Reg | Ryan Greives | P | 18 | 6-4 | 190 | R | R | - | | Benton Central (Oxford,IN) | |
| 48 | 1422 | June-Reg | Dennis Winn | | 17 | 6-2 | 165 | R | R | A | | Home School (Bowling Green,Ky) | |