3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | SpVgg Unterhaching | 19 | 14 | 3 | 2 | 30:11 | +19 | 45:9 | ▲ | |
| 2 | 1. FC Union Berlin | 19 | 12 | 6 | 1 | 33:10 | +23 | 42:9 | ▼ | |
| 3 | Fortuna Düsseldorf | 19 | 11 | 6 | 2 | 28:15 | +13 | 39:12 | – | |
| 4 | FC Bayern München II | 19 | 10 | 6 | 3 | 33:18 | +15 | 36:15 | – | |
| 5 | BSV Kickers Emden | 19 | 10 | 5 | 4 | 29:21 | +8 | 35:17 | ▲ | |
| 6 | Kickers Offenbach | 19 | 9 | 7 | 3 | 25:14 | +11 | 34:16 | ▼ | |
| 7 | SC Paderborn 07 | 19 | 9 | 6 | 4 | 29:12 | +17 | 33:18 | ▼ | |
| 8 | FC Rot-Weiß Erfurt | 19 | 9 | 6 | 4 | 30:22 | +8 | 33:18 | ▼ | |
| 9 | SV Sandhausen | 19 | 8 | 7 | 4 | 32:20 | +12 | 31:19 | ▲ | |
| 10 | VfB Stuttgart II | 19 | 9 | 4 | 6 | 32:20 | +12 | 31:22 | ▼ | |
| 11 | Eintracht Braunschweig | 19 | 8 | 6 | 5 | 33:23 | +10 | 30:21 | – | |
| 12 | SV Werder Bremen II | 19 | 8 | 6 | 5 | 34:26 | +8 | 30:21 | – | |
| 13 | SG Dynamo Dresden | 19 | 8 | 6 | 5 | 26:22 | +4 | 30:21 | – | |
| 14 | Wuppertaler SV | 19 | 8 | 4 | 7 | 24:23 | +1 | 28:25 | – | |
| 15 | SSV Jahn Regensburg | 19 | 8 | 4 | 7 | 20:23 | -3 | 28:25 | ▲ | |
| 16 | VfR Aalen | 19 | 6 | 9 | 4 | 24:23 | +1 | 27:21 | ▼ | |
| 17 | FC Erzgebirge Aue | 19 | 7 | 5 | 7 | 20:18 | +2 | 26:26 | – | |
| 18 | FC Carl Zeiss Jena | 19 | 6 | 8 | 5 | 23:27 | -4 | 26:23 | ▼ | |
| 19 | SV Wacker Burghausen | 19 | 7 | 4 | 8 | 22:28 | -6 | 25:28 | – | |
| 20 | SV Stuttgarter Kickers | 19 | 4 | 6 | 9 | 21:32 | -11 | 18:33 | – |