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1/64-finals
1/32-finals
1/16-finals
1/8-finals
Quarter-finals
Semi-finals
Final
2008/09
1/64-finals
| 1 | CSKA Moscow | Bye | |
| 3 | Torpedo Moscow | Bye | |
| 4 | S. Kostroma | Vladimir | 0 : 1 |
| 5 | Luch | Bye | |
| 7 | Volga Tver | Vol.-Ratmir | 2 : 1 |
| 8 | Bye | Baltika | |
| 9 | Vityaz | Bye | |
| 10 | Bye | Sportakademklub | |
| 12 | Bye | Spartak Nalchik | |
| 13 | Lipetsk | FK Luchovicy | 2 : 0 |
| 14 | Bye | Ulyanovsk | |
| 16 | Bye | Lokomotiv Moscow | |
| 17 | Spartak Moscow | Bye | |
| 19 | Kursk | Dynamo Voronezh | 2 : 0 |
| 20 | Bye | D. Bryansk | |
| 21 | Energomash Belgorod | Bye | |
| 22 | Bye | FK Rostov | |
| 24 | Bye | Shinnik Yaroslavl | |
| 25 | SKA Rostov | Bye | |
| 26 | Krasnodar | Taganrog | 1 : 4 |
| 28 | Bye | Khimki | |
| 29 | Kuban | Bye | |
| 30 | Bye | Chernomorets Novorossijsk | |
| 32 | Bye | Dynamo Moscow | |
| 33 | FC Moscow | Bye | |
| 35 | Volgar-Astrakhan | R. Volgograd | 2 : 1 |
| 36 | Bye | Alania Vladikavkaz | |
| 37 | FK Anzi Makhackala | Bye | |
| 38 | Bye | Mashuk | |
| 40 | Bye | Akhmat Grozny | |
| 41 | Volga N. Novgorod | Lada Togliatti | 5 : 1 |
| 42 | Bye | Nosta | |
| 44 | Bye | Saturn Ramenskoye | |
| 45 | Kamaz | Bye | |
| 46 | Bye | Ural | |
| 48 | Bye | Tomsk | |
| 49 | FK Novosibirsk | Bye | |
| 50 | Bye | Dynamo Barnaul | |
| 52 | Bye | Zenit | |
| 53 | Orenburg | Alnas Almetevsk | 3 : 0 |
| 54 | Bye | FC Novokuznetsk | |
| 56 | Bye | Krylya Sovetov | |
| 57 | Amkar | Bye | |
| 59 | Zvezda Irkutsk | Bye | |
| 60 | Bye | SKA Khabarovsk | |
| 61 | Smena Komsomolsk | Amur | 1 : 0 |
| 62 | FK Sibir Novosibirsk 2 | Yenisey | 1 : 2 |
| 64 | Bye | Rubin Kazan |
1/32-finals
| 1 | CSKA Moscow | Bye | |
| 2 | Torpedo Moscow | Vladimir | 0 : 4 |
| 3 | Luch | Bye | |
| 4 | Volga Tver | Baltika | 1 : 3 |
| 5 | Vityaz | Sportakademklub | 3 : 1 |
| 6 | Bye | Spartak Nalchik | |
| 7 | Lipetsk | Ulyanovsk | 3 : 0 |
| 8 | Bye | Lokomotiv Moscow | |
| 9 | Spartak Moscow | Bye | |
| 10 | Kursk | D. Bryansk | 0 : 1 |
| 11 | Energomash Belgorod | FK Rostov | 3 : 0 |
| 12 | Bye | Shinnik Yaroslavl | |
| 13 | SKA Rostov | Taganrog | 3 : 0 |
| 14 | Bye | Khimki | |
| 15 | Kuban | Chernomorets Novorossijsk | 1 : 0 |
| 16 | Bye | Dynamo Moscow | |
| 17 | FC Moscow | Bye | |
| 18 | Volgar-Astrakhan | Alania Vladikavkaz | 2 : 3 |
| 19 | FK Anzi Makhackala | Mashuk | 3 : 0 |
| 20 | Bye | Akhmat Grozny | |
| 21 | Volga N. Novgorod | Nosta | 1 : 0 |
| 22 | Bye | Saturn Ramenskoye | |
| 23 | Kamaz | Ural | 2 : 1 |
| 24 | Bye | Tomsk | |
| 25 | FK Novosibirsk | Dynamo Barnaul | 4 : 1 |
| 26 | Bye | Zenit | |
| 27 | Orenburg | FC Novokuznetsk | 1 : 0 |
| 28 | Bye | Krylya Sovetov | |
| 29 | Amkar | Bye | |
| 30 | Zvezda Irkutsk | SKA Khabarovsk | 0 : 4 |
| 31 | Smena Komsomolsk | Yenisey | 3 : 2 |
| 32 | Bye | Rubin Kazan |
1/16-finals
| 1 | CSKA Moscow | Vladimir | 4 : 1 |
| 2 | Luch | Baltika | 0 : 3 |
| 3 | Vityaz | Spartak Nalchik | 2 : 1 |
| 4 | Lipetsk | Lokomotiv Moscow | 0 : 2 |
| 5 | Spartak Moscow | D. Bryansk | 2 : 1 |
| 6 | Energomash Belgorod | Shinnik Yaroslavl | 0 : 1 |
| 7 | SKA Rostov | Khimki | 3 : 2 |
| 8 | Kuban | Dynamo Moscow | 0 : 1 |
| 9 | FC Moscow | Alania Vladikavkaz | 3 : 1 |
| 10 | FK Anzi Makhackala | Akhmat Grozny | 2 : 3 |
| 11 | Volga N. Novgorod | Saturn Ramenskoye | 2 : 1 |
| 12 | Kamaz | Tomsk | 1 : 5 |
| 13 | FK Novosibirsk | Zenit | 1 : 0 |
| 14 | Orenburg | Krylya Sovetov | 2 : 3 |
| 15 | Amkar | SKA Khabarovsk | 2 : 1 |
| 16 | Smena Komsomolsk | Rubin Kazan | 1 : 2 |
1/8-finals
| 1 | CSKA Moscow | Baltika | 1 : 0 |
| 2 | Vityaz | Lokomotiv Moscow | 0 : 1 |
| 3 | Spartak Moscow | Shinnik Yaroslavl | 2 : 1 |
| 4 | SKA Rostov | Dynamo Moscow | 0 : 2 |
| 5 | FC Moscow | Akhmat Grozny | 3 : 0 |
| 6 | Volga N. Novgorod | Tomsk | 2 : 3 |
| 7 | FK Novosibirsk | Krylya Sovetov | 2 : 0 |
| 8 | Amkar | Rubin Kazan | 0 : 1 |
Quarter-finals
| 1 | CSKA Moscow | Lokomotiv Moscow | 1 : 0 |
| 2 | Spartak Moscow | Dynamo Moscow | 0 : 3 |
| 3 | FC Moscow | Tomsk | 2 : 1 |
| 4 | FK Novosibirsk | Rubin Kazan | 0 : 2 |
Semi-finals
| 1 | CSKA Moscow | Dynamo Moscow | 3 : 2 |
| 2 | FC Moscow | Rubin Kazan | 0 : 1 |
Final
| 1 | CSKA Moscow | Rubin Kazan | 1 : 0 |
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