2006 MLB Draft: Boston Red Sox
Total Picks: 54 (College: 26, High School: 19, Juco: 9, Other: 0)
Position Players: 27 Pitchers: 27
Players signed indicated in Bold
| Round | Overall | Player | Position | School | State |
| 1 | 27 | Jason Place | of | Wren HS, Piedmont, S.C. | SC |
| 1 | 28 | Daniel Bard | rhp | North Carolina | NC |
| 1S | 40 | Kris Johnson | lhp | Wichita State | KS |
| 1S | 44 | Caleb Clay | rhp | Cullman (Ala.) HS | AL |
| 2 | 71 | Justin Masterson | rhp | San Diego State | CA |
| 3 | 83 | Aaron Bates | 1b | North Carolina State | NC |
| 3 | 103 | Bryce Cox | rhp | Rice | TX |
| 4 | 133 | Jon Still | c | North Carolina State | BC |
| 5 | 163 | Dustin Richardson | lhp | Texas Tech | TX |
| 6 | 193 | Zach Daeges | 3b | Creighton | NE |
| 7 | 223 | Kris Negron | ss | Cosumnes River (Calif.) JC | CA |
| 8 | 253 | Rafael Cabreja | of | Monroe HS, New York | NY |
| 9 | 283 | Ryan Kalish | of | Red Bank (N.J.) Catholic HS | NJ |
| 10 | 313 | Kyle Snyder | rhp | Wellington (Fla.) Community HS | FL |
| 11 | 343 | Brandon Belt | lhp | Hudson HS, Lufkin, Texas | TX |
| 12 | 373 | Ryan Khoury | ss | Utah | UT |
| 13 | 403 | Jordan Craft | rhp | Dallas Baptist | TX |
| 14 | 433 | Matt LaPorta | 1b | Florida | FL |
| 15 | 463 | Jorge Jimenez | 3b | Porterville (Calif.) JC | CA |
| 16 | 493 | Ty Weeden | c | Santa Fe HS, Edmond, Okla. | OK |
| 17 | 523 | Josh Reddick | of | Middle Georgia JC | GA |
| 18 | 553 | Lars Anderson | 1b | Jesuit HS, Carmichael, Calif. | CA |
| 19 | 583 | Richie Lentz | rhp | Washington | WA |
| 20 | 613 | Kyle Gilligan | ss | Etobicoke Collegiate Institute, Toronto | ON |
| 21 | 643 | Brian Steinocher | rhp | Stephen F. Austin | TX |
| 22 | 673 | Michael Christl | rhp | Bradley | IL |
| 23 | 703 | Paul Smyth | of | San Diego State | CA |
| 24 | 733 | Robert Phares | rhp | Shelton State (Ala.) CC | AL |
| 25 | 763 | Sam Gleason | rhp | Lamar (Colo.) CC | CO |
| 26 | 793 | Chad Gross | 1b | Claremont (Calif.) HS | CA |
| 27 | 823 | Brantley New | rhp | Mercer | GA |
| 28 | 853 | Carmine Giardina | lhp | Durant HS, Plant City, Fla. | FL |
| 29 | 883 | Devin Foreman | 1b | Hales Franciscan HS, Chicago | IL |
| 30 | 913 | Ryne Lawson | rhp | West Alabama | AL |
| 31 | 943 | Logan Shafer | of | Cuesta (Calif.) JC | CA |
| 32 | 973 | Mike Chambers | 2b | Franklin Pierce (N.H.) College | NH |
| 33 | 1003 | Jeffrey Rea | 2b | Mississippi State | MS |
| 34 | 1033 | Bryan Morgado | lhp | Florida Christian HS, Tallahassee, Fla. | FL |
| 35 | 1063 | Jeremy Rahman | of | Hazelwood Central HS, Florissant, Mo. | MO |
| 36 | 1093 | Darren Blocker | 3b | Connors State (Okla.) JC | OK |
| 37 | 1123 | Justin Markes | lhp | Owensboro (Ky.) Catholic HS | KY |
| 38 | 1153 | Travis Beazley | rhp | Randolph-Macon (Va.) College | VA |
| 39 | 1183 | Jordan Abruzzo | c | San Diego | CA |
| 40 | 1213 | Corey Davisson | c | West HS, Fresno, Calif. | CA |
| 41 | 1243 | Pete Tountas | ss | Jefferson (Mo.) CC | MO |
| 42 | 1272 | Doug Graybill | lhp | Sarasota (Fla.) HS | FL |
| 43 | 1301 | Jeff Vincent | of | Niagara | NY |
| 44 | 1330 | Andrew Leary | rhp | Sierra Vista HS, Las Vegas | NV |
| 45 | 1359 | Jake McCarter | rhp | Alabama | AL |
| 46 | 1387 | Junior Rodriguez | 3b | Coral Gables (Fla.) HS | FL |
| 47 | 1415 | Nick Hill | lhp | Army | NY |
| 48 | 1443 | Josh Papelbon | rhp | North Florida | FL |
| 49 | 1471 | P.J. Thomas | rhp | Wabash Valley (Ill.) CC | IL |
| 50 | 1499 | Darrell Fisherbaugh | rhp | Hawaii | HI |
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