| 1 | 9 | June-Reg | Barry Zito | P | 21 | 6-4 | 205 | L | L | MLB | 2000-2009 | USC | $1,590,000 |
| 2 | 60 | June-Reg | Ryan Ludwick | OF | 20 | 6-3 | 205 | R | L | MLB | 2002-2009 | UNLV | |
| 3 | 93 | June-Reg | Jorge Soto | C | 21 | 6-0 | 210 | R | R | A+ | | Troy University | |
| 4 | 123 | June-Reg | Keith Surkont | P | 22 | 6-2 | 200 | R | R | AA | | Williams College | $70,000 |
| 5 | 153 | June-Reg | Darin Moore | P | 22 | 6-0 | 195 | R | R | AA | | University of the Pacific | |
| 6 | 183 | June-Reg | Mario Ramos | P | 21 | 5-11 | 180 | L | L | MLB | 2003-2003 | Rice University | |
| 7 | 213 | June-Reg | Josh Hochgesang | IF | 22 | 6-3 | 210 | R | R | AA | | Stanford University | |
| 8 | 243 | June-Reg | Justin Lehr | P | 21 | 6-1 | 200 | R | R | MLB | 2004-2009 | USC | |
| 9 | 273 | June-Reg | Kirk Asche | OF | 21 | 6-2 | 190 | R | R | AA | | Jacksonville University | |
| 10 | 303 | June-Reg | Justin Sobchuk | P | 18 | 6-2 | 195 | L | R | Rookie | | Sehome (Bellingham,WA) | |
| 11 | 333 | June-Reg | Michael Wenner | CF | 20 | 6-1 | 190 | R | R | A+ | | Rider University | |
| 12 | 363** | June-Reg | Jay Garthwaite | OF | 18 | 6-2 | 215 | R | R | AAA | - | Kent-Meridian (Kent,WA) | |
| 13 | 393 | June-Reg | Jason Pomar | P | | | | R | R | A- | | University of South Carolina | |
| 14 | 423 | June-Reg | Alvyn Ellis | IF | | 6-3 | | R | R | A- | | Clackamas Community College | |
| 15 | 453 | June-Reg | Anthony Cicero | C | | | 0 | | | - | | Cleveland (Reseda,CA) | |
| 16 | 483 | June-Reg | Matt Allegra | OF | 17 | 6-3 | 195 | R | R | AA | - | Lake Mary (Lake Mary,FL) | |
| 17 | 513 | June-Reg | Bryan Mazur | P | 21 | 6-0 | 175 | L | L | AA | | University of North Carolina | |
| 18 | 543 | June-Reg | Gary Keller | RF | 22 | 5-10 | 170 | R | R | A+ | | University of Alabama | |
| 19 | 573 | June-Reg | Jason Clements | SS | 21 | 5-11 | 170 | B | R | AAA | | Oral Roberts University | |
| 20 | 603 | June-Reg | Matthew Gage | P | 21 | 6-5 | 205 | R | R | A- | | Eastern Illinois University | |
| 21 | 633 | June-Reg | Cade Sanchez | P | 22 | 6-0 | 205 | L | R | A+ | | University of Texas | |
| 22 | 663** | June-Reg | Edmund Muth | OF | 21 | 6-0 | 198 | L | L | A+ | | Stanford University | |
| 23 | 693 | June-Reg | Mike Lockwood | OF | 22 | 6-0 | 190 | L | L | AAA | | Ohio State University | |
| 24 | 723 | June-Reg | Brad Henderson | 2B | | | 0 | | | A- | | University of Mississippi | |
| 25 | 753** | June-Reg | Fernando De Aza | P | 18 | 6-3 | 200 | R | R | Ind | | Colegio Universario Del E Carolina (PR) | |
| 26 | 783 | June-Reg | Jacob Beckman | P | 20 | 6-2 | 180 | R | R | A+ | | Glen Oaks Community College | |
| 27 | 813 | June-Reg | Donald Atencio | P | 17 | 6-4 | 190 | R | R | A- | | Kirtland Central (Kirtland,NM) | |
| 28 | 843 | June-Reg | Nathan Hilton | P | | | 0 | | | A- | | Iowa State University | |
| 29 | 873** | June-Reg | Andre Marshall | OF | 18 | 6-5 | 205 | B | R | A | | Walla Walla Community College | |
| 30 | 903 | June-Reg | Jonathan Edge | CF | | | 0 | | | - | | University of Tampa | |
| 31 | 933 | June-Reg | Kris Mancini | CF | | | 0 | | | - | | Community College of Rhode Island | |
| 32 | 963 | June-Reg | Micah Dunphy | P | 19 | 6-1 | 180 | L | L | Rookie | | Sauk Valley Community College | |
| 33 | 993 | June-Reg | Alex Coleman | | 17 | 6-3 | 210 | R | R | College | | Poly (Long Beach,CA) | |
| 34 | 1023 | June-Reg | Geoff Comfort | OF | 19 | 6-0 | 210 | R | R | A+ | | College of San Mateo | |
| 35 | 1053 | June-Reg | Darvin Withers | P | 19 | 6-2 | 190 | R | R | A+ | | Spartanburg Methodist College | |
| 36 | 1083 | June-Reg | Jerry Knox | | 19 | 6-2 | 210 | L | R | Ind | | Oakland (Mufreesboro,TN) | |
| 37 | 1113 | June-Reg | Jorge Ortiz | 3B | 18 | 6-4 | 190 | R | R | Rookie | | Miguel Melendez Munoz (Cayey,PR) | |
| 38 | 1143 | June-Reg | Frank James | | 18 | 6-1 | 180 | R | L | Ind | | Navarro College | |
| 39 | 1173 | June-Reg | Brandon Bahr | P | | | 0 | | | - | | Gulf Coast (Naples,FL) | |
| 40 | 1203 | June-Reg | Jared Joaquin | P | | | 0 | | | - | | Lower Columbia Community College | |
| 41 | 1233 | June-Reg | James Cole | P | | | 0 | | | - | | Navarro College | |
| 42 | 1261 | June-Reg | Kellyn Shafer | | 19 | | | R | R | College | | Lane College | |
| 43 | 1288 | June-Reg | Zach Gordon | | | | | | | Ind | | Moorpark College | |
| 44 | 1315 | June-Reg | Eric Kitchen | | | | | | | College | | Durango (Las Vegas,NV) | |
| 45 | 1341 | June-Reg | William Zeier | RF | | | 0 | | | - | | Laney College | |