| Pick | Overall | Team | Player | Position | School | State |
| 1 | 1012 | Washington Nationals | Shane McCatty | RHP | Oakland | Mich. |
| 2 | 1013 | Seattle Mariners | Scott Griggs | RHP | San Ramon Valley HS, Danville, Calif. | Calif. |
| 3 | 1014 | San Diego Padres | Josh Cephas | RHP | Southern Nazarene (Okla.) | Okla. |
| 4 | 1015 | Pittsburgh Pirates | Zac Fuesser | LHP | Walters State (Tenn.) CC | Tenn. |
| 5 | 1016 | Baltimore Orioles | Malcolm Clapsaddle | RHP | Oviedo (Fla.) HS | Fla. |
| 6 | 1017 | San Francisco Giants | Brandon Kirby | OF | Lake Wales (Fla.) HS | Fla. |
| 7 | 1018 | Atlanta Braves | Arby Fields | OF | Los Osos HS, Rancho Cucamonga, Calif. | Calif. |
| 8 | 1019 | Cincinnati Reds | Forest Cannon | RHP | UC Santa Barbara | Calif. |
| 9 | 1020 | Detroit Tigers | Derek Kline | RHP | Millersville (Pa.) | Pa. |
| 10 | 1021 | Colorado Rockies | Brandon Whitby | C | Prairie View A&M | Texas |
| 11 | 1022 | Kansas City Royals | Justin Trapp | SS | Fairfield Central HS, Winnsboro, S.C. | S.C. |
| 12 | 1023 | Oakland Athletics | Dylan Brown | OF | Oklahoma State | Okla. |
| 13 | 1024 | Texas Rangers | Jared Prince | OF | Washington State | Wash. |
| 14 | 1025 | Cleveland Indians | Westley Moss | OF | Nevada | Nev. |
| 15 | 1026 | Arizona Diamondbacks | Patrick Cooper | RHP | Des Moines Area CC | Iowa |
| 16 | 1027 | Los Angeles Dodgers | Justin Dignelli | RHP | George Washington | D.C. |
| 17 | 1028 | Florida Marlins | Isaac Morales | LHP | Cal State Los Angeles | Calif. |
| 18 | 1029 | St. Louis Cardinals | David Kington | RHP | Southern Illinois | Ill. |
| 19 | 1030 | Toronto Blue Jays | Jonathan Fernandez | SS | Guilford Tech (N.C.) CC | N.C. |
| 20 | 1031 | Houston Astros | Scott Migl | RHP | Texas A&M | Texas |
| 21 | 1032 | Minnesota Twins | Ricky Claudio | RHP | American HS, Hialeah, Fla. | Fla. |
| 22 | 1033 | Chicago White Sox | Alex Farotto | LHP | South Carolina | S.C. |
| 23 | 1034 | New York Mets | Cam Maron | C | Hicksville (N.Y.) HS | N.Y. |
| 24 | 1035 | New York Yankees | Jake Petricka | RHP | Indiana State | Ind. |
| 25 | 1036 | Milwaukee Brewers | Mike Ojala | RHP | Rice | Texas |
| 26 | 1037 | Philadelphia Phillies | A.J. Griffin | RHP | San Diego | Calif. |
| 27 | 1038 | Boston Red Sox | Jimmy Patterson | LHP | Central Arizona JC | Ariz. |
| 28 | 1039 | Tampa Bay Rays | Kyle Spraker | SS | Loyola Marymount | Calif. |
| 29 | 1040 | Chicago Cubs | Rett Varner | RHP | Texas-Arlington | Texas |
| 30 | 1041 | Los Angeles Angels | Ryan Cisterna | RHP | Arkansas | Ark. |