| 1 | 24 | June-Reg | Kurt Ainsworth | P | 20 | 6-3 | 192 | R | R | MLB | 2001-2004 | Louisiana State University | $1,300,000 |
| 1 | 39 | June-Reg | Jerome Williams | P | 17 | 6-3 | 180 | R | R | MLB | 2003-2007 | Waipahu (Waipahu, HI) | $832,500 |
| 2 | 62 | June-Reg | John Thomas | P | 17 | 6-2 | 190 | L | L | AAA | | Righetti (Santa Maria,CA) | |
| 2 | 75 | June-Reg | Jack Taschner | P | 21 | 6-3 | 190 | L | L | MLB | 2005-2009 | University of Wisconsin | |
| 3 | 108 | June-Reg | Sean McGowan | IF | 22 | 6-6 | 240 | R | R | AAA | | Boston College | $127,500 |
| 4 | 138 | June-Reg | Jeremy Cunningham | P | 20 | 6-5 | 190 | R | R | A+ | | Cal Poly | |
| 5 | 168 | June-Reg | Ryan Cox | P | 22 | 6-3 | 210 | R | R | AAA | | Southern Illinois University | $50,000 |
| 6 | 198 | June-Reg | Ryan Pene | OF | | | 0 | | | A- | | Dixie State College of Utah | |
| 7 | 228 | June-Reg | Joe Jester | IF | 20 | 5-10 | 180 | R | R | AAA | | University of Arkansas | |
| 8 | 258 | June-Reg | Kevin Vent | P | 22 | 6-0 | 185 | R | R | AAA | | University of Arkansas | |
| 9 | 288 | June-Reg | Josh Cook | SS | 21 | 6-2 | 195 | R | R | A+ | | Yuba Community College | |
| 10 | 318 | June-Reg | Anthony Yacco | P | 18 | 6-3 | 220 | R | R | A+ | | Mahopac (Mahopac,NY) | |
| 11 | 348 | June-Reg | Jeff Verplancke | P | 21 | 6-3 | 200 | R | R | AAA | | Cal State Los Angeles | |
| 12 | 378** | June-Reg | Ronnie Merrill | IF | 20 | 6-1 | 185 | B | R | AAA | | University of Tampa | |
| 13 | 408 | June-Reg | Fletcher Lee | P | 23 | 6-1 | 190 | R | R | A+ | | Lewis and Clark College | |
| 14 | 438** | June-Reg | Mike Meyer | P | 21 | 6-2 | 180 | R | R | A+ | | University of Arizona | |
| 15 | 468 | June-Reg | Harold Featherstone | P | 22 | 6-2 | 175 | R | R | A+ | | North Carolina A&T State University | |
| 16 | 498 | June-Reg | Micah Holst | OF | 22 | 6-2 | 200 | R | R | AAA | | Missouri State University | |
| 17 | 528 | June-Reg | Vance Cozier | P | 21 | 6-6 | 245 | R | R | AA | | St. Bonaventure University | |
| 18 | 558 | June-Reg | Brian Meagher | P | | | 0 | | | A- | | College of San Mateo | |
| 19 | 588 | June-Reg | Ryan Cheo | P | | | | | | College | | Saddleback College | |
| 20 | 618 | June-Reg | Anthony Turco | C | 19 | 5-9 | 175 | L | R | AA | | St. Petersburg College | |
| 21 | 648 | June-Reg | Ryan Luther | C | 22 | 6-10 | 185 | R | R | AAA | | Lewis and Clark College | |
| 22 | 678 | June-Reg | Jason Barrow | OF | | | 0 | | | - | | Chemeketa Community College | |
| 23 | 708 | June-Reg | Michael Zirelli | P | | | 0 | | | A+ | | Cal Poly | |
| 24 | 738** | June-Reg | Bill Murphy | P | 18 | 6-0 | 190 | L | L | MLB | 2007-2009 | Arlington (Riverside,CA) | $0 |
| 25 | 768** | June-Reg | Andrew Edwards | P | 17 | 6-5 | 215 | R | R | A- | | Christ the King (Flushing,NY) | |
| 26 | 798 | June-Reg | Kevin Alexander | IF | 18 | 5-10 | 162 | R | R | A+ | - | Modesto Junior College | |
| 27 | 828 | June-Reg | Troy Gustafson | LF | 19 | 6-3 | 190 | R | R | A+ | | Blaine (Blaine,MN) | |
| 28 | 858 | June-Reg | Lars Hansen | C | | | 0 | | | - | | University of Hawaii | |
| 29 | 888 | June-Reg | Troy Ransom | P | 20 | 6-2 | 180 | R | R | A+ | | South Mountain Community College | |
| 30 | 918 | June-Reg | Ryan Davis | | 20 | 6-2 | 190 | L | L | A+ | | Cosumnes River College | |
| 31 | 948 | June-Reg | Scott Daeley | | 22 | 5-10 | 178 | R | R | AA | | Wake Forest University | |
| 32 | 978** | June-Reg | Tim Gilhooly | OF | 17 | 6-3 | 210 | R | R | A- | - | San Ramon Valley (Danville,CA) | |
| 33 | 1008 | June-Reg | Kavonski Chatman | P-CF | | | 0 | | | - | | Northeast Texas Community College | |
| 34 | 1038** | June-Reg | Scott Shoemaker | | 17 | 6-4 | 215 | R | R | AAA | | Granite Hills (El Cajon,CA) | |
| 35 | 1068 | June-Reg | Robert Lorona | SS | | | 0 | | | - | | Hayden (Winkelman,AZ) | |
| 36 | 1098 | June-Reg | Bryan Lang | OF | | | 0 | | | - | | Scottsdale Community College | |
| 37 | 1128 | June-Reg | Chris Norris | P | 19 | 6-4 | 225 | L | R | - | | Central Arizona College | |
| 38 | 1158** | June-Reg | Drew Endicott | P | 18 | 6-3 | 180 | R | R | AA | | Carthage (Carthage,MO) | |
| 39 | 1188 | June-Reg | Paul Turco | | 22 | 5-11 | 162 | B | R | A+ | | Auburn University | |
| 40 | 1218** | June-Reg | Travis Veracka | | | | | | | College | | University of Massachusetts | |
| 41 | 1247 | June-Reg | Winston Woods | CF | | | 0 | | | - | | Broward College | |
| 42 | 1275** | June-Reg | Jason Hickman | | 20 | 6-2 | 205 | L | L | Ind | | Ball State University | |
| 43 | 1302 | June-Reg | Brett Cayton | P | 15 | 6-2 | 215 | R | R | College | | Fountain Valley (Fountain Valley,CA) | |
| 44 | 1329 | June-Reg | Daniel August | P | | | 0 | | | - | | St. Petersburg College | |
| 45 | 1354** | June-Reg | Chad Ashlock | P | 20 | 6-2 | 200 | R | R | A- | | University of Texas | |
| 46 | 1378 | June-Reg | Wes Faust | P | 21 | 6-8 | 240 | R | R | A | | Oklahoma Baptist University | |
| 47 | 1402 | June-Reg | Oscar Vargas | | 19 | 5-11 | 175 | R | R | Ind | | Chabot College | |
| 48 | 1426 | June-Reg | Jamie Aloy | 1B | | | 0 | | | - | | University of Hawaii | |
| 49 | 1449 | June-Reg | Josh Sousa | P | | | 0 | | | - | | Modesto Junior College | |
| 50 | 1470 | June-Reg | Brian Grochol | OF | | | 0 | | | A- | | Canada College | |