2ND ROUND (28 TEAMS -> 14 WINNERS)
Between the 10 winners of the 1st round (in italics), 12 league champions of stronger countries and 6 second of even stronger countries (Ukraine, Israel, Turkey, Belgium, Czech Republic and Switzerland)
| Home | Away | Aggr | |
| Pyunik (Armenia/1) – Shaktar (Ukraine/2) | 1-3 | 0-1 | 1-4 |
| Gorica (Slovenia/1) – Kobenhavn (Denmark/1) | 1-2 | 5-0 | 6-2 |
| Neftchi (Azerbaijan/1) – CSKA Moskva (Russia/1) | 0-0 | 0-2 | 0-2 |
| HJK (Finland/1) – M. Tel-Aviv (Israel/2) | 0-0 | 0-1 | 0-1 |
| Tirana (Albania/1) – Ferencvaros (Hungary/1) | 2-3 | 1-0 | 3-3 |
| WIT (Georgia/1) – Wisla (Poland/1) | 2-8 | 0-3 | 2-11 |
| Hadjuk (Croatia/1) – Shelbourne (Ireland/1) | 3-2 | 0-2 | 3-4 |
| Djugarden (Sweden/1) – Kaunas (Lithuania/1) | 0-0 | 2-0 | 2-0 |
| Skonto (Latvia/1) – Trabzonspor (Turkey/2) | 1-1 | 0-3 | 1-4 |
| Club Brugge (Belgium/2) – Loko Plovdiv (Bulgaria/1) | 2-0 | 4-0 | 6-0 |
| Zilina (Slovakia/1) – Dinamo Bucuresti (Romania/1) | 0-1 | 0-1 | 0-2 |
| APOEL (Cyprus/1) – Sparta (Czech Republic/2) | 2-2 | 1-2 | 3-4 |
| Rosenborg (Norway/1) – Sheriff (Moldavia/1) | 2-1 | 2-0 | 4-1 |
| Young Boys (Switz./2) – Red Star Belgrade (Serbia/1) | 2-2 | 0-3 | 2-5 |
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