Through games of Sunday March 31, 2013
| # | School (1st votes) | Rec | Pts | Prev. |
| 1 | Cortland State (14) | 17-4 | 601 | 2 |
| 2 | Linfield (5) | 20-4 | 587 | 1 |
| 3 | Marietta (3) | 12-4 | 545 | 5 |
| 4 | Salisbury (1) | 17-5 | 522 | 4 |
| 5 | Ramapo (1) | 13-1 | 504 | 9 |
| 6 | Kean | 16-5 | 492 | 6 |
| 7 | St. Thomas | 12-4 | 471 | 7 |
| 8 | Christopher Newport | 24-8-1 | 420 | 8 |
| 9 | Trinity (Texas) (1) | 24-7 | 408 | 3 |
| 10 | Wheaton (Mass.) | 12-5 | 373 | 10 |
| 11 | Johns Hopkins | 16-2 | 333 | 17 |
| 12 | Keystone | 15-5 | 311 | 13 |
| 13 | Texas-Tyler | 23-7 | 300 | 14 |
| 14 | UW-Whitewater | 9-3 | 264 | 15 |
| 15 | Webster | 13-5 | 248 | 18 |
| 16 | Manchester | 15-3-1 | 211 | 16 |
| 17 | George Fox | 19-7 | 158 | rv |
| 18 | Shenandoah | 15-6 | 147 | 12 |
| 19 | UW-Oshkosh | 11-1 | 144 | 24 |
| 20 | Birmingham-Southern | 20-8 | 127 | 22 |
| 21 | St. Joseph's (Maine) | 10-5 | 125 | 11 |
| 22 | Cal Lutheran | 19-6-1 | 105 | rv |
| 23 | Augustana | 13-3 | 99 | 19 |
| 24 | Pomona-Pitzer | 19-7 | 98 | rv |
| 25 | Haverford | 14-2 | 81 | 21 |
Dropped out: No. 20 Western New England, No. 23
UW-Stevens Point, No. 25 Huntingdon
Others receiving votes: Western New Eng. 61,
UW-Stevens Point 60, Bridgewater (Va.) 39, Wittenberg 33, Ill.
Wesleyan 28, Ithaca 27, Eastern Conn. St. 24, Wartburg 22, St.
Scholastica 22, Texas Lutheran 19, Neumann 18, Southern Me. 17,
Millsaps 16, St. Joseph's (Brkln) 14, Spalding 12, Benedictine 9,
UW-La Crosse 8, La Roche 4, Baldwin Wallace 4, Suffolk 4,
Heidelberg 2, Aurora 2, Huntingdon 2, Otterbein 2, Rhodes 1, Rowan
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.