| Wednesday 30th July 2003 | |||
| 1st Leg | |||
| Bohemians | 0-1 | Rosenborg | |
| CSKA Moscow | 1-2 | FK Vardar Skopje | |
| FBK Kaunas | 0-4 | Celtic | |
| FC Copenhagen | 5-1 | Sliema Wanderers | |
| Leotar | 1-2 | Slavia Prague | |
| MSK Zilina | 1-0 | Maccabi Tel-Aviv | |
| MTK Budapest | 3-1 | HJK Helsinki | |
| NK Maribor | 1-1 | Dinamo Zagreb | |
| Partizan Belgrade | 1-1 | Djurgardens | |
| Pyunik Yerevan | 0-2 | CSKA Sofia | |
| Rapid Bucharest | 0-0 | Anderlecht | |
| Sheriff Tiraspol | 0-0 | Shakhtar Donetsk | |
| SK Tirana | 1-5 | Grazer AK | |
| Wisla Krakow | 6-2 | Omonia Nicosia | |
| Wednesday 6th August 2003 | |||
| 2nd Leg | |||
| Anderlecht | 3-2 | Rapid Bucharest | (3-2) |
| Celtic | 1-0 | FBK Kaunas | (5-0) |
| CSKA Sofia | 1-0 | Pyunik Yerevan | (3-0) |
| Dinamo Zagreb | 2-1 | NK Maribor | (3-2) |
| Djurgardens | 2-2 | Partizan Belgrade | (3-3) |
| (Partizan Belgrade won on away goals) | |||
| FK Vardar Skopje | 1-1 | CSKA Moscow | (3-2) |
| Grazer AK | 2-1 | SK Tirana | (7-2) |
| HJK Helsinki | 1-0 | MTK Budapest | (2-3) |
| Maccabi Tel-Aviv | 1-1 | MSK Zilina | (1-2) |
| Omonia Nicosia | 2-2 | Wisla Krakow | (4-8) |
| Rosenborg | 4-0 | Bohemians | (5-0) |
| Shakhtar Donetsk | 2-0 | Sheriff Tiraspol | (2-0) |
| Slavia Prague | 2-0 | Leotar | (4-1) |
| Sliema Wanderers | 0-6 | FC Copenhagen | (1-11) |
