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| 25/09/2012 | 14:30 | NK Vrsar | - | Dinamo Zagreb | 0:3 (0:3) | |
| 14:30 | HNK Gorica | - | NK Inter Zaprešić | 3:0 (1:0) | ||
| 16:00 | Lokomotiva Zagreb | - | HNK Segesta | 4:2 (3:1) | ||
| 26/09/2012 | NK Libertas | - | NK Varaždin | 3:0 dec. | ||
| NK Zelina | - | NK Karlovac | 3:0 dec. | |||
| 14:30 | NK Slunj | - | Hajduk Split | 0:4 | ||
| 14:30 | Zrinski Tordinci | - | NK Zagreb | 0:4 | ||
| 14:30 | NK Vinodol | - | HNK Cibalia | 0:2 | ||
| 14:30 | NK Novalja | - | NK Osijek | 0:1 | ||
| 14:30 | NK Ivančica | - | Slaven Belupo | 1:2 (0:0) | ||
| 14:30 | NK GOŠK Dubrovnik | - | HNK Šibenik | 4:2 pso | ||
| 14:30 | NK Nedelišće | - | HNK Rijeka | 1:0 (0:0, 0:0) aet | ||
| 14:30 | NK Koprivnica | - | NK Pomorac | 2:1 aet | ||
| 14:30 | NK Višnjevac | - | NK Istra 1961 | 1:2 | ||
| 15:30 | NK Zadar | - | NK Konavljanin Cilipi | 2:0 | ||
| 17:00 | RNK Split | - | NK Zagora Unešić | 5:1 (1:0) |
