| 1. Round | 15/08/1999 | Hertha BSC | - | Hansa Rostock | 5:2 | ||||
| 4. Round | 10/09/1999 | Hansa Rostock | - | SSV Ulm 1846 | 2:1 | ||||
| 5. Round | 17/09/1999 | SC Freiburg | - | Hansa Rostock | 5:0 | ||||
| 6. Round | 25/09/1999 | Hansa Rostock | - | TSV 1860 München | 0:0 | ||||
| 8. Round | 16/10/1999 | Hansa Rostock | - | Eintracht Frankfurt | 3:1 | ||||
| 9. Round | 22/10/1999 | Hansa Rostock | - | Arminia Bielefeld | 2:1 |  |
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| 10. Round | 29/10/1999 | Werder Bremen | - | Hansa Rostock | 2:1 | ||||
| 11. Round | 05/11/1999 | Hansa Rostock | - | Hamburger SV | 3:3 | ||||
| 13. Round | 27/11/1999 | Hansa Rostock | - | SpVgg Unterhaching | 1:1 | ||||
| 18. Round | 04/02/2000 | Hansa Rostock | - | Hertha BSC | 0:1 | ||||
| 21. Round | 20/02/2000 | SSV Ulm 1846 | - | Hansa Rostock | 1:1 | |
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| 22. Round | 25/02/2000 | Hansa Rostock | - | SC Freiburg | 1:1 | ||||
| 27. Round | 02/04/2000 | Hansa Rostock | - | Werder Bremen | 1:1 | ||||
| 28. Round | 07/04/2000 | Hamburger SV | - | Hansa Rostock | 1:0 | ||||
| 30. Round | 16/04/2000 | SpVgg Unterhaching | - | Hansa Rostock | 1:1 |  |
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| 31. Round | 22/04/2000 | Hansa Rostock | - | MSV Duisburg | 3:1 | |
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| 32. Round | 29/04/2000 | Bayern München | - | Hansa Rostock | 4:1 |
Croatia