| 1 | 20 | June-Reg | C.C. Sabathia | P | 17 | 6-7 | 250 | L | L | MLB | 2001-2009 | Vallejo (Vallejo,CA) | $1,300,000 |
| 2 | 63 | June-Reg | Zach Sorensen | SS | 21 | 6-0 | 190 | B | R | MLB | 2003-2005 | Wichita State University | |
| 3 | 93 | June-Reg | Scott Pratt | OF | 21 | 5-10 | 185 | L | R | AAA | - | Auburn University | |
| 4 | 123 | June-Reg | Ronald Marietta | P | 20 | 6-0 | 190 | L | L | A | - | St. John's University | |
| 5 | 153 | June-Reg | Ryan Drese | P | 22 | 6-3 | 220 | R | R | MLB | 2001-2006 | University of California | |
| 6 | 183 | June-Reg | Tyler Minges | OF | 18 | 6-0 | 185 | R | R | AAA | | Ross (Hamilton,OH) | |
| 7 | 213 | June-Reg | Brody Percell | P | 22 | 6-2 | 200 | L | L | A+ | | Oregon State University | |
| 8 | 243 | June-Reg | Chris Reinike | P | 21 | 6-0 | 195 | R | R | AAA | | University of Mississippi | |
| 9 | 273 | June-Reg | Paul Day | 3B | 21 | 6-1 | 200 | R | R | A- | | Long Beach State University | |
| 10 | 303 | June-Reg | Michael McPadden | P | 18 | 6-4 | 185 | L | R | Rookie | | Port St. Lucie (Port St. Lucie,FL) | |
| 11 | 333 | June-Reg | Jake Reynolds | | | | | | | Rookie | | Giles County (Pulaski,TN) | |
| 12 | 363 | June-Reg | Donald Suttles | P | 21 | 6-2 | 185 | R | R | A | | Western Carolina University | |
| 13 | 393 | June-Reg | Matt Wade | P | 18 | 6-2 | 195 | R | R | A+ | | Parkview (Liburn,GA) | |
| 14 | 423 | June-Reg | Brian Jackson | P | 20 | 6-4 | 190 | R | R | A+ | | USC | |
| 15 | 453 | June-Reg | Matt White | P | 20 | 6-1 | 180 | R | L | MLB | 2003-2005 | Clemson University | |
| 16 | 483 | June-Reg | Richard Matsko | P | 21 | 6-2 | 210 | R | R | A+ | | Shippensburg University of Pennsylvania | |
| 17 | 513 | June-Reg | Mark Koeth | P | 20 | 6-3 | 215 | R | R | A+ | | Brookhaven (Carrolton,TX) | |
| 18 | 543 | June-Reg | T.T. Gallaher | OF | 20 | 5-10 | 185 | R | R | A+ | | University of New Haven | |
| 19 | 573 | June-Reg | David Raymer | | 19 | 5-10 | 190 | L | R | College | | Sacramento State | |
| 20 | 603 | June-Reg | Barry Patton | C | 22 | 6-2 | 220 | R | R | A- | | University of Mississippi | |
| 21 | 633** | June-Reg | Michael DiRosa | C | 18 | 5-11 | 195 | R | R | AA | | Coral Gables (Coral Gables,FL) | |
| 22 | 663 | June-Reg | Carey Novits | P | 22 | 6-1 | 185 | L | L | A- | | Cal State Northridge | |
| 23 | 693 | June-Reg | J.J. Sherrill | 2B | 17 | 5-7 | 170 | B | R | AA | | Monterey (Monterey,CA) | |
| 24 | 723 | June-Reg | Tom Bost | OF | 22 | 6-2 | 220 | L | R | AA | | Louisiana Tech University | |
| 25 | 753 | June-Reg | Eric Maleski | P | 21 | 6-2 | 195 | R | R | A+ | | Benedictine (Cleveland,OH) | |
| 26 | 783 | June-Reg | Chris MacMillan | 3B | 22 | 6-2 | 195 | R | R | A- | | Cal State Northridge | |
| 27 | 813 | June-Reg | Jeff Depippo | C | 22 | 5-7 | 170 | R | R | AA | | USC | |
| 28 | 843 | June-Reg | Rudy Rosales | P | 21 | 6-3 | 220 | R | R | Rookie | | Pima Community College | |
| 29 | 873 | June-Reg | Ruben Escobar | P | 22 | 6-1 | 185 | R | R | AA | | The Masters H.S. (Hesperia,CA) | |
| 30 | 903 | June-Reg | Michael Pursell | 2B | 22 | 6-0 | 187 | L | R | A | | Tulane (Pensacola,FL) | |
| 31 | 933 | June-Reg | Marques Esquerra | SS | 22 | 6-1 | 185 | B | R | A+ | | Point Loma Nazarene University | |
| 32 | 963 | June-Reg | Craig Brown | P | 21 | 5-9 | 170 | L | L | A- | | Tulane University | |
| 33 | 993** | June-Reg | Brian Strelitz | P | 18 | 6-2 | 200 | R | R | AA | | Temple City (Temple City,CA) | |
| 34 | 1022** | June-Reg | James Jurries | IF | 19 | 6-0 | 195 | R | R | AAA | | Brazoswood (Clute,TX) | |
| 35 | 1053** | June-Reg | Randon Ho | P | | | 0 | | | - | | University of Hawaii | |
| 36 | 1083 | June-Reg | Matthew Ramie | 1B | | | 0 | | | - | | Castle (Kaneohe,HI) | |
| 37 | 1113 | June-Reg | Micah Simmons | | | | | | | Ind | | Paxon (Jacksonville,FL) | |
| 38 | 1143 | June-Reg | Brian Minks | P | | | 0 | | | - | | Neosho County (Mulvane,KS) | |
| 39 | 1173 | June-Reg | Darrel Berck | P | 21 | 6-0 | 170 | R | R | Rookie | | Palomar College | |
| 40 | 1203 | June-Reg | Dan Guillory | P | 22 | 6-3 | 205 | R | R | AA | | Louisiana State University | |
| 41 | 1233 | June-Reg | Brian Sullivan | | | | | | | College | | Port St. Lucie (Port St. Lucie,FL) | |
| 42 | 1262** | June-Reg | Blake Whealy | OF | 18 | 5-11 | 170 | R | R | A+ | | Oak Park-River Forest (Oak Park,IL) | |
| 43 | 1290 | June-Reg | Dana Thomas | P | | | 0 | | | - | | Fork Union Military Academy (Fork Union,VA) | |
| 44 | 1316 | June-Reg | Miguel Hernandez | 1B | 15 | 6-2 | 220 | R | R | Rookie | | Nuestra Seno (Bayamon,PR.) | |
| 45 | 1340 | June-Reg | Eric Bush | P | | | 0 | | | - | | Washington (Pensacola,FL) | |
| 46 | 1363 | June-Reg | Brandon Mauer | C | | | | | | - | | Bellevue Community College | |
| 47 | 1384 | June-Reg | Kevin Spaulding | | 16 | 6-0 | 190 | L | R | Ind | | Anacortes (Anacortes,WA) | |
| 48 | 1404 | June-Reg | Garth Blumberg | | 19 | 5-10 | 190 | | | College | | Hoquiam (Taholah,WA) | |
| 49 | 1421** | June-Reg | Kevin Hooper | IF | 21 | 5-9 | 155 | R | R | MLB | 2005-2006 | Wichita State University | |
| 50 | 1437 | June-Reg | Omar Moraga | 2B-3B | 21 | 5-9 | 180 | L | R | A+ | | University of Arizona | |