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<!–* — indicates the player has signed. Those players under contract will attend a mini-camp in Mesa, Ariz., and
will be assigned to a Cub rookie league team in Boise or Mesa.
–>
| Pick | Name | Pos | School |
| 66 | Grant Johnson | RHP | Notre Dame |
| 96 | Mark Reed | C | Bonita HS (Calif.) |
| 126 | Chris Shaver | LHP | William and Mary |
| 156 | Adrian Ortiz | CF | Puerto Rico BB Academy |
| 186 | Timothy Layden | LHP | Duke |
| 216 | Mitchell Atkins | RHP | Northeast Guilford HS |
| 246 | Eric Patterson | 2B | Georgia Tech |
| 276 | Ryan Norwood | 1B | East Carolina |
| 306 | Samuel Fuld | CF | Stanford |
| 336 | Jon Hunton | RHP | Lamar |
| 366 | Sean Gallagher | RHP | St. Thomas Aquinas HS (Fla.) |
| 396 | Ryan Moorer | RHP | Veterans Memorial HS (Mass.) |
| 426 | Eli Iorg | LF | Tennessee |
| 456 | Alfred Joseph | CF | Foy H. Moody HS |
| 486 | Alfred Mathes | LHP | Western Michigan |
| 516 | Jerry Blevins | LHP | Dayton |
| 546 | Jake Marsello | RHP | Boston College |
| 576 | Micah Owings | RHP | Georgia Tech |
| 606 | David Taylor | LHP | Baylor |
| 636 | Willson Fenton | RHP | Washington |
| 666 | Walter Diaz | SS | Braddock HS |
| 696 | Chris Gaskin | 1B | Manhattan College |
| 726 | Jeff Culpepper | RF | Gonzaga |
| 756 | Casey Erickson | RHP | Glenwood HS |
| 786 | Paul Cinder | RHP | Lake Mary HS |
| 816 | Jason Koskow | RHP | Babson College |
| 846 | Jon Douillard | C | Vanderbilt |
| 876 | Michael Svetlic | 2B | UCLA |
| 906 | Russell Canzler | 3B | Hazleton Area HS |
| 936 | Jesus Estrada | RHP | Grayson County College |
| 966 | Cody Gilbert | 3B | Vincennes Lincoln HS |
| 996 | Randy Brown | RF | Jonesboro HS |
| 1026 | James Bamberg | C | Winter Haven HS |
| 1056 | Drew O’Connell | RHP | Barrington HS |
| 1086 | Colby Wark | RHP | Redmond HS |
| 1116 | Michael Hyle | RHP | Georgia |
| 1146 | Kurt Eichorn | LF | Kent St. |
| 1176 | Trenton Luyster | LHP | Ohio St. |
| 1206 | Marcus Crockett | CF | St. Bernard HS |
| 1236 | Kenn Kasparek | RHP | Weimer HS |
| 1265 | Ryan Morgan | 3B | Boston College |
| 1294 | Adam Daniels | LHP | E. Oklahoma St. CC |
| 1323 | Matthew Zane Green | RF | Clemson |
| 1352 | Chris Dunkin | C | LaPorte HS |
| 1381 | Greg Fudacz | LHP | Cle Elum-Roslyn HS |
| 1410 | Andrew Liebel | RHP | Damien HS |
| 1438 | Olin Wick | C | Puget Sound |
| 1466 | Brandon Harmon | RHP | Columbia Basin JC |
| 1494 | Gerald Miller | CF | Prairie View A&M |
