| 2. Round | 26/03/2006 | FK Rostov | - | FK Moskva | 4:0 | ||||
| 6. Round | 23/04/2006 | FK Rostov | - | Shinnik Yaroslavl | 0:0 | ||||
| 7. Round | 30/04/2006 | FK Tom Tomsk | - | FK Rostov | 3:1 |  |
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| 8. Round | 06/05/2006 | FK Rostov | - | FK Saturn | 0:2 |  |
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| 3. Round | 17/05/2006 | Zenit St. Petersburg | - | FK Rostov | 1:1 | |
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| 10. Round | 10/07/2006 | CSKA Moskva | - | FK Rostov | 1:2 | ||||
| 16. Round | 20/08/2006 | FK Rostov | - | Rubin Kazan | 2:1 | ||||
| 17. Round | 27/08/2006 | FK Moskva | - | FK Rostov | 4:0 | ||||
| 18. Round | 10/09/2006 | FK Rostov | - | Zenit St. Petersburg | 1:3 | ||||
| 19. Round | 16/09/2006 | Torpedo Moskva | - | FK Rostov | 0:2 | ||||
| 20. Round | 23/09/2006 | FK Rostov | - | Dinamo Moskva | 2:1 | |
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| 21. Round | 30/09/2006 | Shinnik Yaroslavl | - | FK Rostov | 1:6 | |
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| 22. Round | 15/10/2006 | FK Rostov | - | FK Tom Tomsk | 2:1 | ||||
| 23. Round | 21/10/2006 | FK Saturn | - | FK Rostov | 0:0 | ||||
| 24. Round | 25/10/2006 | FK Rostov | - | FK Amkar Perm | 1:1 | |
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| 25. Round | 28/10/2006 | FK Rostov | - | CSKA Moskva | 1:2 | ||||
| 26. Round | 04/11/2006 | Krylia Sovetov | - | FK Rostov | 1:0 | ||||
| 27. Round | 08/11/2006 | FK Rostov | - | Luch-Energiya Vladivostok | 1:0 | ||||
| 29. Round | 18/11/2006 | FK Rostov | - | Spartak Moskva | 3:4 |
Malawi