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| # | Team | P | W | D | L | Goals | Pts |
|---|---|---|---|---|---|---|---|
| 1 | FC Cologne | 34 | 19 | 11 | 4 | 53:20 | 68 |
| 2 | Paderborn | 34 | 18 | 8 | 8 | 63:48 | 62 |
| 3 | SpVgg Greuther Fürth | 34 | 17 | 9 | 8 | 64:38 | 60 |
| 4 | 1. FC Kaiserslautern | 34 | 15 | 9 | 10 | 55:39 | 54 |
| 5 | Karlsruher SC | 34 | 12 | 14 | 8 | 47:34 | 50 |
| 6 | Fortuna Düsseldorf | 34 | 13 | 11 | 10 | 45:44 | 50 |
| 7 | TSV 1860 München | 34 | 13 | 9 | 12 | 38:41 | 48 |
| 8 | FC St. Pauli | 34 | 13 | 9 | 12 | 44:49 | 48 |
| 9 | Union Berlin | 34 | 11 | 11 | 12 | 48:47 | 44 |
| 10 | FC Ingolstadt 04 | 34 | 11 | 11 | 12 | 34:33 | 44 |
| 11 | VfR Aalen | 34 | 11 | 11 | 12 | 36:39 | 44 |
| 12 | SV Sandhausen | 34 | 12 | 8 | 14 | 29:35 | 44 |
| 13 | FSV Frankfurt | 34 | 11 | 8 | 15 | 46:51 | 41 |
| 14 | Erzgebirge Aue | 34 | 11 | 8 | 15 | 42:54 | 41 |
| 15 | VfL Bochum | 34 | 11 | 7 | 16 | 30:43 | 40 |
| 16 | Arminia Bielefeld | 34 | 9 | 8 | 17 | 40:58 | 35 |
| 17 | Dynamo Dresden | 34 | 5 | 17 | 12 | 36:53 | 32 |
| 18 | Energie Cottbus | 34 | 6 | 7 | 21 | 35:59 | 25 |