| Mannschaft | Spiele | gew. | unent. | verl. | Tore | Torv. | Punkte | veränd. |
| 1. 1.FC Köln | 23 | 14 | 6 | 3 | 47:19 | + 28 | 48 |  |
| 2. VfL Bochum | 23 | 12 | 4 | 7 | 38:32 | + 6 | 40 | |
| 3. FC Energie Cottbus | 23 | 12 | 2 | 9 | 43:28 | + 15 | 38 | |
| 4. Borussia Mönchengladbach | 23 | 9 | 8 | 6 | 35:27 | + 8 | 35 | |
| 5. Alemannia Aachen | 23 | 9 | 8 | 6 | 34:37 | - 3 | 35 |  |
| 6. Tennis Borussia Berlin | 23 | 8 | 10 | 5 | 30:26 | + 4 | 34 |  |
| 7. 1.FC Nürnberg | 22 | 9 | 6 | 7 | 33:36 | - 3 | 33 | |
| 8. Waldhof Mannheim | 23 | 7 | 10 | 6 | 32:31 | + 1 | 31 | |
| 9. FSV Mainz 05 | 23 | 7 | 9 | 7 | 29:27 | + 2 | 30 | |
| 10. Rot-Weiß Oberhausen | 23 | 7 | 9 | 7 | 22:22 | + 0 | 30 | |
| 11. SpVgg. Greuther Fürth | 23 | 6 | 11 | 6 | 23:25 | - 2 | 29 | |
| 12. Hannover 96 | 23 | 7 | 7 | 9 | 33:33 | + 0 | 28 | |
| 13. Chemnitzer FC | 22 | 7 | 7 | 8 | 29:31 | - 2 | 28 | |
| 14. FC St.Pauli | 23 | 5 | 10 | 8 | 24:30 | - 6 | 25 | |
| 15. Kickers Offenbach |
23 | 5 |
9 | 9 |
23:34 |
- 11 |
24 | |
| 16. Stuttgarter Kickers | 23 | 5 | 6 | 12 | 31:45 | - 14 | 21 | |
| 17. Fortuna Köln | 23 | 4 | 9 | 10 | 21:34 | - 13 | 21 | |
| 18. Karlsruher SC | 23 | 3 | 9 | 11 | 26:36 | - 10 | 18 | |
Ergebnisse 1999/2000