| Pick | Overall | Team | Player | Position | School | State |
| 1 | 986 | Washington Nationals | Ryan Sherriff | LHP | West Los Angeles JC | Calif. |
| 2 | 987 | Pittsburgh Pirates | Justin Ennis | LHP | Louisiana State-Shreveport | La. |
| 3 | 988 | Baltimore Orioles | Steven Mazur | RHP | Notre Dame | Ind. |
| 4 | 989 | Kansas City Royals | Cole Lohden | RHP | Southern Arkansas | Ark. |
| 5 | 990 | Cleveland Indians | Logan Thompson | 2B | Palm Beach (Fla.) CC | Fla. |
| 6 | 991 | Arizona Diamondbacks | Andrew Whittington | C | Southern Arkansas | Ark. |
| 7 | 992 | New York Mets | Hunter Carnevale | RHP | Pacific | Calif. |
| 8 | 993 | Houston Astros | Michael Ness | RHP | Duke | N.C. |
| 9 | 994 | San Diego Padres | Daniel Ottone | RHP | Western Carolina | N.C. |
| 10 | 995 | Oakland Athletics | Sean Murphy | RHP | Keystone (Pa.) | Pa. |
| 11 | 996 | Toronto Blue Jays | Melvin Garcia | OF | Monroe HS, New York | N.Y. |
| 12 | 997 | Cincinnati Reds | David Garner | RHP | Niles (Mich.) HS | Mich. |
| 13 | 998 | Chicago White Sox | Jamaal Hollis | RHP | Miami (Ohio) | Ohio |
| 14 | 999 | Milwaukee Brewers | William Kankel | LHP | Houston | Texas |
| 15 | 1000 | Chicago Cubs | Matt Stites | RHP | Jefferson (Mo.) CC | Mo. |
| 16 | 1001 | Tampa Bay Rays | Scott Simon | RHP | Central Valley HS, Spokane, Wash. | Wash. |
| 17 | 1002 | Seattle Mariners | D.J. Peterson | 3B | Gilbert (Ariz.) HS | Ariz. |
| 18 | 1003 | Detroit Tigers | Brennan Smith | RHP | Bowling Green State | Ohio |
| 19 | 1004 | Atlanta Braves | Albert Minnis | LHP | Lawrence (Kan.) HS | Kan. |
| 20 | 1005 | Minnesota Twins | Justin Parker | LHP | Consumnes River (Calif.) JC | Calif. |
| 21 | 1006 | Texas Rangers | Matt Hill | LHP | Georgia Perimeter JC | Ga. |
| 22 | 1007 | Florida Marlins | D'Andre Toney | OF | Hardaway HS, Columbus, Ga. | Ga. |
| 23 | 1008 | San Francisco Giants | Jim Birmingham | LHP | Coastal Carolina | S.C. |
| 24 | 1009 | St. Louis Cardinals | Joey Bergman | 2B | College of Charleston | S.C. |
| 25 | 1010 | Colorado Rockies | Jordan Ballard | 1B | Virginia Military Institute | Va. |
| 26 | 1011 | Philadelphia Phillies | Bob Stumpo | C | West Chester (Pa.) | Pa. |
| 27 | 1012 | Los Angeles Dodgers | Brett Lee | LHP | Bishop State (Ala.) CC | Ala. |
| 28 | 1013 | Boston Red Sox | Mark Donham | RHP | Jupiter (Fla.) Community HS | Fla. |
| 29 | 1014 | Los Angeles Angels | Eric Cendejas | RHP | Cal State Stanislaus | Calif. |
| 30 | 1015 | New York Yankees | Michael Hachadorian | RHP | San Diego Mesa JC | Calif. |