| Tuesday 13th July 2004 | |||
| 1st Leg | |||
| FK Pobeda Prilep | 1-3 | Pyunik Yerevan | |
| NK Siroki Brijeg | 2-1 | Neftchi Baku | |
| Sliema Wanderers | 0-2 | FBK Kaunas | |
| Wednesday 14th July 2004 | |||
| 1st Leg | |||
| FC Gomel | 0-2 | SK Tirana | |
| Flora Tallinn | 2-4 | HIT Gorica | |
| KR Reykjavik | 2-2 | Shelbourne | |
| Linfield | 0-1 | HJK Helsinki | |
| Sheriff Tiraspol | 2-0 | Jeunesse Esch | |
| Skonto Riga | 4-0 | Rhyl | |
| WIT Georgia Tbilisi | 5-0 | HB Torshavn | |
| Wednesday 21st July 2004 | |||
| 2nd Leg | |||
| FBK Kaunas | 4-1 | Sliema Wanderers | (6-1) |
| HB Torshavn | 3-0 | WIT Georgia Tbilisi | (3-5) |
| HIT Gorica | 3-1 | Flora Tallinn | (7-3) |
| HJK Helsinki | 1-0 | Linfield | (2-0) |
| Jeunesse Esch | 1-0 | Sheriff Tiraspol | (1-2) |
| Neftchi Baku | 1-0 | NK Siroki Brijeg | (2-2) |
| (Neftchi Baku won on away goals) | |||
| Pyunik Yerevan | 1-1 | FK Pobeda Prilep | (4-2) |
| Rhyl | 1-3 | Skonto Riga | (n) (1-7) |
| Shelbourne | 0-0 | KR Reykjavik | (2-2) |
| (Shelbourne won on away goals) | |||
| SK Tirana | 0-1 | FC Gomel | (2-1) |
