| Rnd | Ovl | Phase | Player Name | $$ | Pos | Age | Born | Ht | Wt | B | T | High Level | MLB Years | Drafted From |
| 1 | 2 | June-Reg | Alex Gordon | $$ | 3b | 21 | 2/10/1984 | 6-1 | 220 | L | R | MLB | 2007-2008 | University of Nebraska |
| 2 | 50 | June-Reg | Jeff Bianchi | $$ | ss | 18 | 10/5/1986 | 6-0 | 175 | R | R | A+ | | Lampeter Strasburg High School (Lampeter,PA) |
| 3 | 82 | June-Reg | Chris Nicoll | $$ | RHP | 21 | 10/30/1983 | 6-1 | 190 | R | R | A+ | | University of California-Irvine |
| 4 | 112 | June-Reg | Joe Dickerson | | of | 18 | 10/3/1986 | 6-1 | 190 | L | L | A+ | | Esperanza High School (Anaheim,CA) |
| 5 | 142 | June-Reg | Shawn Hayes | | ss | 20 | 11/5/1984 | 6-4 | 220 | L | R | Rookie | | Franklin Pierce College |
| 6 | 172 | June-Reg | Ryan Dipietro | | lhp | 20 | 7/21/1984 | 6-0 | 175 | L | L | A | | Eastern Connecticut State University |
| 7 | 202 | June-Reg | Brent Fisher | | LHP | 17 | 8/6/1987 | 6-2 | 185 | L | L | A | | Tolleson Union High School (Tolleson,AZ) |
| 8 | 232 | June-Reg | Nicholas Doscher | | C | 18 | 5/20/1987 | 6-2 | 205 | R | R | A | | Moore Catholic High School (Staten Island,NY) |
| 9 | 262 | June-Reg | Kiel Thibault | | c | 21 | 3/2/1984 | 6-0 | 195 | R | R | AA | | Gonzaga University |
| 10 | 292 | June-Reg | Jeff Howell | | C | 22 | 4/1/1983 | 6-0 | 200 | R | R | AA | | Florida Southern College |
| 11 | 322 | June-Reg | Michael Penn | | rhp | 23 | 4/21/1982 | 6-4 | 205 | R | R | A+ | | University of Michigan |
| 12 | 352 | June-Reg | Cody Harkcom | | rhp | 21 | 12/15/1983 | 6-1 | 180 | R | R | A | | New Mexico Junior College |
| 13 | 382 | June-Reg | Andrew Larsen | | of | 22 | 12/14/1982 | 6-0 | 200 | R | R | A+ | | Stony Brook University |
| 14 | 412 | June-Reg | Anton Sabatini | | CF | 22 | 4/1/1983 | 6-0 | 195 | R | L | A | | Erskine College |
| 15 | 442 | June-Reg | Brady Everett | | C | 21 | 7/8/1983 | 6-0 | 205 | R | R | A+ | | Washington State University |
| 16 | 472 | June-Reg | Mario Santiago | | rhp | 19 | 12/16/1985 | 6-2 | 210 | R | R | A+ | | Baton Rouge (La. CC ) |
| 17 | 502 | June-Reg | Miguel Vasquez | | SS | 18 | 11/25/1986 | 6-1 | 190 | R | R | Rookie | | DeWitt Clinton High School (Bronx,NY) |
| 18 | 532 | June-Reg | Paul Raglione | | rhp | 18 | 1/15/1987 | 6-5 | 195 | R | R | Rookie | | Grant High School (Portland,OR) |
| 19 | 562 | June-Reg | Zane Chavez | | c | 18 | 12/30/1986 | 5-10 | 180 | L | R | - | | Fallbrook High School (Fallbrook,CA) |
| 20 | 592 | June-Reg | Bryan Casey | $$ | rhp | 19 | 6/5/1986 | 6-1 | 200 | R | R | Rookie | | Arizona Western College |
| 21 | 622 | June-Reg | David Henninger | | RHP | 21 | 8/23/1983 | 6-8 | 212 | R | R | A | | Messiah College |
| 22 | 652 | June-Reg | Justin Bristow | | ss | 18 | 3/6/1987 | 6-4 | 200 | R | R | College | | Mills Godwin High School (Richmond,VA) |
| 23 | 682 | June-Reg | Matt Kniginyzky | | rhp | 22 | 10/5/1982 | 6-3 | 185 | L | R | A+ | | High Point University |
| 24 | 712 | June-Reg | Joshua Colafemina | | SS | 22 | 8/25/1982 | 5-8 | 150 | R | R | Rookie | | College of Saint Rose |
| 25 | 742 | June-Reg | Kevin Bulger | | rhp | 22 | 2/16/1983 | 6-4 | 195 | R | R | Rookie | | College of Charleston |
| 26 | 772 | June-Reg | Jake Mclintock | | RHP | 22 | 1/26/1983 | 6-1 | 190 | R | R | Rookie | | San Diego State University |
| 27 | 802 | June-Reg | Jase Turner | | 1b | 22 | 2/22/1983 | 6-2 | 225 | L | R | A | | Pomona-Pitzer Colleges |
| 28 | 832 | June-Reg | Josh Morgan | | of | 20 | 7/29/1984 | 6-3 | 210 | R | R | Rookie | | Oklahoma Baptist University |
| 29 | 862 | June-Reg | Brandon Brantley | | RHP | 22 | 8/13/1982 | 6-4 | 225 | R | R | Rookie | | University of Science and Arts (Okla.) |
| 30 | 892 | June-Reg | Jeremy Jirschele | | 2b | 22 | 11/14/1982 | 5-9 | 195 | R | R | A+ | | University of Wisconsin, Oshkosh |
| 31 | 922 | June-Reg | Pedro Lopez | | ss | 18 | 10/31/1986 | 5-9 | 160 | B | R | A- | | Universidad del Turabo (Toa Baja,PR) |
| 32 | 952** | June-Reg | Michael Dubee | | RHP | 19 | 1/12/1986 | 6-2 | 177 | R | R | A+ | | Okaloosa-Walton College |
| 33 | 982 | June-Reg | Daniel Gutierrez | | rhp | 18 | 3/8/1987 | 6-0 | 175 | R | R | A | | Rubidoux High School (Riverside,CA) |
| 34 | 1012 | June-Reg | Oscar Marrero | | C | 18 | 1/26/1987 | 5-11 | 180 | B | R | Rookie | | Juan Antonio Corretjer (Ciales,PR) |
| 35 | 1042 | June-Reg | Luke Burnett | | rhp | 18 | 12/10/1986 | 6-8 | 260 | R | R | College | | Carthage High School (Carthage,TX) |
| 36 | 1072** | June-Reg | Matthew Klimas | | c | 17 | 7/3/1987 | 5-11 | 185 | R | R | A | | Broken Arrow High School (Broken Arrow,OK) |
| 37 | 1102 | June-Reg | Nickolas Love | | OF | 18 | 11/19/1986 | 6-0 | 180 | R | R | - | | Enterprise High School (Enterprise,AL) |
| 38 | 1132 | June-Reg | Jacob Myking | | c | 19 | 5/3/1986 | 6-0 | 215 | R | R | - | | San Joaquin Delta College |
| 39 | 1162 | June-Reg | Steve Teno | | lhp | 17 | 9/28/1987 | 6-0 | 155 | R | L | - | | St. Thomas of Villanova High School (LaSalle,ON) |
| 40 | 1191 | June-Reg | Nick Romero | | SS | 25 | 1/12/1980 | 5-10 | 150 | R | R | A- | | Eastlake High School (Chula Vista,CA) |
| 41 | 1220 | June-Reg | Anthony Rodriguez | | ss | 18 | 1/6/1987 | 6-1 | 172 | R | R | - | | Puerto Rico Baseball Academy High School (Gurabo,PR) |
| 42 | 1249** | June-Reg | David McClain | | RHP | 18 | 4/4/1987 | 6-3 | 180 | L | R | - | | North Shore High School (Houston,TX) |
| 43 | 1278 | June-Reg | Tyler Backus | | rhp | 18 | 2/15/1987 | 6-2 | 175 | R | R | - | | Mingus Union High School (Cottonwood,AZ) |
| 44 | 1307 | June-Reg | Mark Serrano | | rhp | | | | | | | - | | Cypress College |
| 45 | 1336** | June-Reg | Eric Martinez | | RHP | 18 | 1/18/1987 | 6-2 | 180 | L | R | - | | Eastlake High School (Chula Vista,CA) |
| 46 | 1365** | June-Reg | Brian Paukovits | | RHP | 18 | 6/29/1987 | 6-7 | 238 | R | R | Rookie | | El Capitan High School (Lakeside,CA) |
| 47 | 1394 | June-Reg | Kip Masuda | | c | 17 | 10/17/1987 | 6-0 | 185 | R | R | College | | Mid-Pacific Institute, Kanoehe, Hawaii |
| 48 | 1422 | June-Reg | Chester Wilson | | 1b | 19 | 6/7/1986 | 5-11 | 215 | R | R | College | | St. Louis High School (Honolulu,HI) |
| 49 | 1449 | June-Reg | Matt Gibbs | | rhp | 20 | 4/24/1985 | 6-3 | 210 | R | R | - | | Modesto Junior College |
| 50 | 1476 | June-Reg | Juan Perez | | RHP | 18 | 5/31/1987 | 6-0 | 150 | R | R | - | | Jose Rojas Cortez (Orocovis,PR) |
| |
