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<!–* — indicates the player has signed. Those players under contract will attend a mini-camp in Tucson, Ariz. and will be assigned to a Sox rookie league team in Bristol, Va. or Phoenix. Top pick Royce Ring was assigned to the Class A team in Winston-Salem, N.C., and No. 2 pick Jeremy Reed was assigned to the Class A team, in Kannapolis, N.C.
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| Pick | Name | Pos | School |
| 15 | Brian
Anderson |
CF | Arizona |
| 52 | Ryan Sweeney | OF | Cedar Rapids (Iowa) Xavier |
| 82 | Clinton King | RF | Southern Mississippi |
| 112 | Robert Valido | SS | Miami Coral Park HS |
| 142 | Matthew Nachreiner | RHP | Round Rock (Tex.) HS |
| 172 | Christopher Kelly | LF | Pepperdine |
| 202 | James Casey | RHP | Azle (Tex.) HS |
| 232 | John Russ | RHP | Frank Phillips College |
| 262 | David Cook | CF | Miami (Ohio) |
| 292 | Fraser Dizard | LHP | Southern California |
| 322 | Richard Brooks | RHP | North Tonawanda (N.Y.) HS |
| 352 | Donald Veal | LHP | Sierra Vista (Ariz.) Buena HS |
| 382 | Wes Hodges | SS | Chattanooga Baylor HS |
| 412 | Ricardo Nanita | CF | Florida International |
| 442 | Gregory Moviel | LHP | Cleveland St. Ignatius |
| 472 | Cody Dickens | RHP | Dobson (N.C.) Surry CC |
| 502 | Guillermo Martinez | SS | Miami Coral Park HS |
| 532 | Cory Haggerty | 2B | Cortland State |
| 562 | Michael Moat | RHP | San Diego State |
| 592 | Jeffrey Schmidt | SS | San Diego Mira Mesa HS |
| 622 | Matthew Lenderman | C | Plano (Tex.) East HS |
| 652 | Travis Doyle | LHP | Grand Rapids CC |
| 682 | John Hurd | RHP | College of Southern Idaho |
| 712 | Burke Baldwin | LHP | Neuqua Valley HS |
| 742 | Antoin Gray | 3B | Southern University |
| 772 | Logan Williamsonl | LHP | Pensacola (Fla.) Catholic HS |
| 802 | Dwayne Pollok | RHP | Texas A&M |
| 832 | Peter Pope | 3B | Meridian CC |
| 862 | Gerardo Cabrera | CF | Miami Dade CC South |
| 892 | Brandon Lowe | 1B | Vidalia (Ga.) HS |
| 922 | Robert Grinestaff | C | Jeffersonville (Ind.) HS |
| 952 | Joshua Morgan | OF | Meridian CC |
| 982 | Alex Acevedo | SS | Dr. Carlos Gonzalez |
| 1012 | Scott Martin | RF | Delaware State |
| 1042 | Sean Thompson | RF | Cal Santa Barbara |
| 1072 | Paul Moviel | RHP | Kishwaukee College |
| 1102 | Neil Giesler | 3B | Okaloosa-Walton JC |
| 1132 | Michael Mendrin | LHP | Central HS |
| 1162 | Jason Sullivan | RHP | Joplin HS |
| 1192 | Matthew Deuchler | C | James Madison |
| 1222 | Rolando Acosta | SS | Pima CC |
| 1251 | Eric
Everly |
LHP | Olney Central JC |
| 1280 | Dustin Shafer | SS | Russell (Ky.) HS |
| 1308 | Brandon Johnson | 2B | Crowder JC |
| 1335 | Mitchell Woolf | RHP | College of Southern Idaho |
| 1362 | Greg Del George | SS | Monsignor Farrell (N.J.) HS |
| 1389 | Richard O’Brien | C | Catholic (Ark.) HS |
| 1416 | Michael Alvarez | RHP | Monsignor Pace (Fla.) HS |
| 1442 | Tim Edmeads | 3B | Buena Regional (N.J.) HS |
| 1468 | Sean Gaston | C | Brownsburg (Ind.) HS |
