| # | Player Name | Pos | Team | Age | Born | Ht | Wt | B-T | High Level | MLB Years | Drafted From | # |
| 981. | J.B. Paxson | c | ARI | 18 | 7/28/1986 | 6-3 | 0 | R-R | College | | Center Grove High School (Greenwood,IN) | 1 |
| 982. | Daniel Gutierrez | rhp | KC | 18 | 3/8/1987 | 6-0 | 175 | R-R | A | | Rubidoux High School (Riverside,CA) | 8 |
| 983. | Julian Henson | c | SEA | 18 | 4/10/1987 | 5-10 | 190 | R-R | AA | | Cordova High School (Cordova,TN) | 1 |
| 984. | Ryan Buchter | lhp | WAN | 18 | 2/13/1987 | 6-3 | 200 | L-L | A- | | Highland Regional High School (Blackwood,NJ) | 2 |
| 985. | Jorge Core | rhp | MIL | 17 | 2/17/1988 | 6-2 | 0 | R-R | - | | Puerto Rico Baseball Academy High School (Gurabo,PR) | 24 |
| 986. | Jeff Tobin | lhp | TOR | 21 | 11/13/1983 | 6-1 | 185 | L-L | - | | University of British Columbia | 7 |
| 987. | Jordan Jarvis | rhp | COL | 18 | 9/20/1986 | 6-3 | 205 | R-R | - | | Arcadia High School (Phoenix,AZ) | 9 |
| 988. | Tyler Reves | c | TB | 21 | 1/15/1984 | 5-11 | 208 | R-R | A+ | | Wharton County Junior College | 13 |
| 989. | Daniel Arizmendi | lhp | NYM | 21 | 6/13/1984 | 5-11 | 200 | L-L | Rookie | | Santa Ana College | 57 |
| 990. | Loren Fraser | rhp | DET | 22 | 8/20/1982 | 6-6 | 235 | R-R | A+ | | University of California-Santa Barbara | 89 |
| 991. | Michael Klindt | of | PIT | 18 | 4/25/1987 | 6-2 | 190 | R-R | - | | Centennial High School (Roswell,GA) | 1 |
| 992. | Leroy Hunt | of | CIN | 17 | 11/28/1987 | 6-6 | 220 | R-R | - | | Linden High School (Linden,CA) | 4 |
| 993. | Tyrone Anu | of | BAL | 18 | 3/13/1987 | 6-2 | 170 | R-R | - | | Colonial High School (Orlando,FL) | 12 |
| 994. | Trevor Mortensen | of | CLE | 22 | 2/12/1983 | 5-10 | 190 | R-R | A+ | | California State University, Fullerton | 221 |
| 995. | Scott Savastano | ss | CHW | 19 | 6/12/1986 | 6-4 | 190 | R-R | - | | Plymouth North High School (Plymouth,MA) | 1 |
| 996. | Adam Howard | c | FLA | 19 | 10/3/1985 | 6-2 | 195 | R-R | A | | St. Louis Community College-Meramec | 61 |
| 997. | Andrez Ibarz | rhp | PHI | 18 | 11/13/1986 | 6-4 | 220 | R-R | - | | Champagnat Catholic High School (Hialeah,FL) | 4 |
| 998. | Adam Gold | rhp | SD | 21 | 10/7/1983 | 6-3 | 185 | R-R | A- | | University of California | 154 |
| 999. | Kevin Gossage | c | TEX | 18 | 2/16/1987 | 6-4 | 190 | R-R | A | | Coronado High School (Colorado Springs,CO) | 1 |
| 1000. | Ben Ferguson | rhp | CHC | 18 | 10/10/1986 | 6-7 | 210 | R-R | - | | Cottonwood High School (Salt Lake City,UT) | 3 |
| 1001. | Matt Singleton | c | OAK | 22 | 1/25/1983 | 6-3 | 185 | R-R | A+ | | Ball State University | 45 |
| 1002. | Chris Todd | 2b | SF | 22 | 9/20/1982 | 5-10 | 170 | B-R | A- | | Coastal Carolina University | 42 |
| 1003. | Marco Albano | ss | LAA | 21 | 8/26/1983 | 5-11 | 215 | R-R | A+ | | Boston College | 32 |
| 1004. | Reid Kelly | rhp | HOU | 18 | 10/31/1986 | 6-2 | 180 | R-R | A | | Desert Mountain High School (Scottsdale,AZ) | 3 |
| 1005. | Brandon Trodick | of | MIN | 18 | 5/4/1987 | 6-2 | 180 | R-R | - | | Cimarron Memorial High School (Las Vegas,NV) | 9 |
| 1006. | Chris LeMay | lhp | LA | 20 | 1/14/1985 | 6-2 | 170 | R-L | - | | Kwantlen College | 5 |
| 1007. | Tyler Flowers | 1b | ATL | 19 | 1/24/1986 | 6-4 | 220 | R-R | A+ | | Chipola College | 120 |
| 1008. | John Hester | c | BOS | 21 | 9/14/1983 | 6-4 | 210 | R-R | AA | | Stanford University | 219 |
| 1009. | Michael Miotkowski | rhp | NYY | 23 | 11/14/1981 | 6-5 | 245 | R-R | - | | Oklahoma City University | 48 |
| 1010. | Scott Vander Weg | rhp | STL | 22 | 12/14/1982 | 6-3 | 210 | R-R | AA | | Lamar University | 55 |
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