Records are from the final 2012 D3baseball.com Top 25
| # | School (1st votes) | Rec | Pts | Prev. |
| 1 | Wheaton (Mass.) (8) | 41-11 | 594 | 2 |
| 2 | St. Thomas (3) | 41-10 | 586 | 3 |
| 3 | Marietta (14) | 48-8 | 578 | 1 |
| 4 | Cortland State | 41-9-1 | 564 | 4 |
| 5 | Whitworth | 31-16-1 | 457 | 8 |
| 6 | Birmingham-Southern | 38-9 | 443 | 10 |
| 7 | Kean | 37-12 | 422 | 6 |
| 8 | Christopher Newport | 34-10 | 411 | 5 |
| 9 | Salisbury | 34-9 | 386 | 11 |
| 10 | Webster | 36-14 | 361 | 7 |
| 11 | Trinity (Texas) | 37-12 | 360 | 13 |
| 12 | Keystone | 37-8 | 333 | 9 |
| 13 | Adrian | 37-10 | 304 | 12 |
| 14 | St. Joseph's (Maine) | 39-7 | 245 | 14 |
| 15 | Western New England | 38-13 | 214 | 17 |
| 16 | Concordia (Texas) | 37-11 | 206 | 15 |
| 17 | UW-La Crosse | 34-11 | 194 | 16 |
| 18 | UW-Whitewater | 33-17 | 191 | 24 |
| 19 | Trinity (Conn.) | 34-11 | 161 | 22 |
| 20 | Ramapo | 35-15 | 147 | 23 |
| 21 | Washington and Jefferson | 36-10 | 119 | 20 |
| 22 | St. Scholastica | 35-11 | 101 | 25 |
| 23 | Shenandoah | 31-13 | 100 | 18 |
| 24 | Aurora | 38-10 | 77 | 19 |
| 25 | Farmingdale State | 32-12 | 66 | rv |
Others receiving votes: UW-Stevens Point 44, Alvernia 30, Washington (Mo.) 28, Illinois Wesleyan 24, Misericordia 22, Mount Union 21, Lynchburg 20, St. John Fisher 18, Rose-Hulman 15, Bridgewater (Va.) 15, North Park 14, Texas-Tyler 14, St. John's (Minn.) 12, Neumann 12, Eastern Conn. St. 12, Manchester 11, Coe 11, Old Westbury 11, La Verne 10, Southern Maine 10, Cal Lutheran 9, Pomona-Pitzer 9, Chapman 8, Rhodes 8, Huntingdon 7, Husson 6, Ithaca 6, Bridgewater St. 5, Penn St.-Behrend 5, Tufts 5, Wooster 4, DePauw 3, Emory 3, Western Conn. St. 3, Rowan 2, Chicago 2, Anderson (Ind.) 2 , Millsaps 2, La Roche 2, Linfield 2, Hope 1, Johns Hopkins 1.
The D3baseball.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. Full members of NCAA Division III are eligible.