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| RNK | School | Record | Conf Record | PF | PA |
| 1 |
Notre Dame |
10-2 |
|
482 |
262 |
| 2 |
Navy |
8-4 |
|
390 |
225 |
| 3 |
Army |
3-9 |
|
258 |
357 |
| 4 |
Nevada Southern |
0-12 |
|
73 |
511 |
| 2006 Conference Winners |
|---|
| IA Independents Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Notre Dame |
10-2 |
|
482 |
262 |
| Sun Belt Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Florida International |
10-2 |
7-0 |
343 |
265 |
| MAC Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Northern Illinois |
12-1 |
8-0 |
422 |
191 |
| WAC Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Boise State |
11-1 |
8-0 |
537 |
237 |
| Mountain West Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Utah |
10-2 |
8-0 |
456 |
220 |
| Pac-10 Winner |
|---|
| School | Record | Conf Record | PF | PA |
| USC |
11-1 |
9-0 |
501 |
224 |
| ACC Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Virginia Tech |
13-0 |
8-0 |
472 |
180 |
| Big East Winner |
|---|
| School | Record | Conf Record | PF | PA |
| West Virginia |
12-0 |
7-0 |
454 |
121 |
| Big 10 Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Ohio State |
11-1 |
7-1 |
474 |
197 |
| Big 12 Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Oklahoma |
12-1 |
7-1 |
574 |
182 |
| SEC Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Auburn |
11-2 |
6-2 |
471 |
184 |
| C-USA Winner |
|---|
| School | Record | Conf Record | PF | PA |
| Southern Miss |
7-6 |
5-3 |
338 |
334 |
