| Northern | ||||||||||||||
| Rk | Team | Affiliate | W | L | Pct | Gbl | RF | RA | Manager | Stadium | Attendance | Top Batter | Top Pitcher | Playoffs |
| 1 | Wilmington Blue Rocks | KC | 89 | 51 | .636 | -- | 691 | 519 | Jeff Garber | Daniel S. Frawley Stadium | 331,545 | Byron Gettis (11) | Ryan Douglass (11) | Lost in Semi-Finals |
| 2 | Lynchburg Hillcats ** | PIT | 87 | 53 | .621 | 2.0 | 700 | 522 | Pete Mackanin | Lynchburg City Stadium | 127,916 | Josh Bonifay (3) | Landon Jacobsen (4) | League Champions |
| 3 | Potomac Cannons | STL | 59 | 81 | .421 | 30.0 | 555 | 646 | Joseph Cunningham | G. Richard Pfitzner Stadi | 182,059 | Johnny Hernandez (8) | Jeremy Cook (25) | |
| 4 | Frederick Keys | BAL | 47 | 92 | .338 | 41.5 | 562 | 760 | Jack Voigt | Harry Grove Stadium | 305,950 | Cory Keylor (17) | Jancy Andrade (9) | |
| Southern | ||||||||||||||
| Rk | Team | Affiliate | W | L | Pct | Gbl | RF | RA | Manager | Stadium | Attendance | Top Batter | Top Pitcher | Playoffs |
| 1 | Myrtle Beach Pelicans | ATL | 79 | 61 | .564 | -- | 555 | 541 | Randy Ingle | BB&T Coastal Field | 200,463 | Bill McCarthy (12) | Chris Waters (1) | Lost in Semi-Finals |
| 2 | Kinston Indians | CLE | 74 | 65 | .532 | 4.5 | 598 | 587 | Ted Kubiak | Grainger Stadium | 133,169 | Corey Smith (9) | Aquiles Pinales (19) | Lost in Finals |
| 3 | Salem Avalanche | COL | 74 | 66 | .529 | 5.0 | 656 | 647 | Stu Cole | Salem Municipal Stadium | 196,347 | Brad Hawpe (1) | Kip Bouknight (2) | |
| 4 | Winston-Salem Warthogs | CHW | 50 | 90 | .357 | 29.0 | 552 | 686 | Razor Shines | Ernie Shore Field | 136,302 | Ruddy Yan (15) | Heath Phillips (3) | |