Through games of Jan. 4, 2009:
| # | Team | W-L | Pts. | Last Week |
| 1 | Wheaton (Ill.) (16) | 11-0 | 614 | 2 |
| 2 | St. Thomas (4) | 10-0 | 594 | 3 |
| 3 | Washington U. (2) | 9-1 | 568 | 4 |
| 4 | UW-Platteville (3) | 12-1 | 551 | 1 |
| 5 | Amherst | 9-0 | 513 | 8 |
| 6 | UW-Stevens Point | 9-2 | 452 | 5 |
| 7 | Augustana | 10-2 | 451 | 9 |
| 8 | Buena Vista | 10-1 | 429 | 10 |
| 9 | UW-Whitewater | 11-2 | 404 | 6 |
| 10 | Elmhurst | 9-2 | 395 | 7 |
| 11 | Capital | 9-1 | 370 | 12 |
| 12 | Ithaca | 10-0 | 317 | 17 |
| 13 | Richard Stockton | 11-1 | 301 | 14 |
| 14 | Carnegie Mellon | 10-1 | 273 | 15 |
| 15 | Whitworth | 11-1 | 238 | 19 |
| 16 | Trinity (Texas) | 11-1 | 214 | 21 |
| 17 | Puget Sound | 9-2 | 210 | 22 |
| 18 | Elms | 10-1 | 182 | 11 |
| 19 | Illinois Wesleyan | 8-3 | 181 | 16 |
| 20 | Mass-Dartmouth | 9-1 | 158 | 24 |
| 21 | Ursinus | 6-3 | 98 | 13 |
| 22 | Roanoke | 10-1 | 96 | — |
| 23 | St. Norbert | 8-1 | 77 | — |
| 24 | Texas-Dallas | 9-1 | 65 | 23 |
| 25 | Anderson | 9-3 | 45 | — |
Dropped out: No. 18 Centre, No. 20 St. Mary's (Md.), No. 25 DeSales.
Others receiving votes: Franklin and Marshall 40, Gettysburg 39, Centre 29, St. Mary's (Md.) 26, William Paterson 26, Middlebury 24, New York University 22, DeSales 21, Mary Hardin-Baylor 19, St. John Fisher 19, Bethel 16, Salem State 14, Worcester Polytech 13, Randolph-Macon 12, Millikin 5, Ohio Northern 3, Wooster 1.
The D3hoops.com Top 25 is voted on by a panel of 25 coaches, Sports Information Directors and media members from across the country, and is published weekly.