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| 1st(1st leg) | Valur Reykjavík | - | AS Monaco | 1:0 (0:0) | ||
| 2nd (2nd leg) | AS Monaco | - | Valur Reykjavík | 2:0 (2:0) | ||
| 1st(1st leg): 06/09/1988 | 2nd (2nd leg): 04/10/1988 | Winner: AS Monaco | ||||
| 1st(1st leg) | BFC Dynamo | - | Werder Bremen | 3:0 (1:0) | ||
| 2nd (2nd leg) | Werder Bremen | - | BFC Dynamo | 5:0 (1:0) | ||
| 1st(1st leg): 06/09/1988 | 2nd (2nd leg): 11/10/1988 | Winner: Werder Bremen | ||||
| 1st(1st leg) | Club Brugge KV | - | Brøndby IF | 1:0 (0:0) | ||
| 2nd (2nd leg) | Brøndby IF | - | Club Brugge KV | 2:1 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Club Brugge KV | ||||
| 1st(1st leg) | Dundalk FC | - | Crvena Zvezda | 0:5 (0:0) | ||
| 2nd (2nd leg) | Crvena Zvezda | - | Dundalk FC | 3:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Crvena Zvezda | ||||
| 1st(1st leg) | Górnik Zabrze | - | Jeunesse Esch | 3:0 (2:0) | ||
| 2nd (2nd leg) | Jeunesse Esch | - | Górnik Zabrze | 1:4 (1:2) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Górnik Zabrze | ||||
| 1st(1st leg) | Hamrun Spartans | - | Nentori Tiranë | 2:1 (0:1) | ||
| 2nd (2nd leg) | Nentori Tiranë | - | Hamrun Spartans | 2:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Nentori Tiranë | ||||
| 1st(1st leg) | Budapest Honved SE | - | Celtic FC | 1:0 (1:0) | ||
| 2nd (2nd leg) | Celtic FC | - | Budapest Honved SE | 4:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Celtic FC | ||||
| 1st(1st leg) | Pezoporikos Larnaca | - | IFK Göteborg | 1:2 (1:1) | ||
| 2nd (2nd leg) | IFK Göteborg | - | Pezoporikos Larnaca | 5:1 (4:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: IFK Göteborg | ||||
| 1st(1st leg) | AE Lárissa | - | Neuchâtel Xamax FC | 2:1 (1:0) | ||
| 2nd (2nd leg) | Neuchâtel Xamax FC | - | AE Lárissa | 3:0 (0:0, 2:1, 2:1) pso | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Neuchâtel Xamax FC | ||||
| 1st(1st leg) | FC Porto | - | HJK Helsinki | 3:0 (2:0) | ||
| 2nd (2nd leg) | HJK Helsinki | - | FC Porto | 2:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: FC Porto | ||||
| 1st(1st leg) | Rapid Wien | - | Galatasaray | 2:1 (1:0) | ||
| 2nd (2nd leg) | Galatasaray | - | Rapid Wien | 2:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Galatasaray | ||||
| 1st(1st leg) | TJ Sparta ČKD Praha | - | CSA Steaua București | 1:5 (1:2) | ||
| 2nd (2nd leg) | CSA Steaua București | - | TJ Sparta ČKD Praha | 2:2 (1:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: CSA Steaua București | ||||
| 1st(1st leg) | Spartak Moskva | - | Glentoran FC | 2:0 (0:0) | ||
| 2nd (2nd leg) | Glentoran FC | - | Spartak Moskva | 1:1 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Spartak Moskva | ||||
| 1st(1st leg) | Real Madrid | - | Moss FK | 3:0 (3:0) | ||
| 2nd (2nd leg) | Moss FK | - | Real Madrid | 0:1 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Real Madrid | ||||
| 1st(1st leg) | Vitosha Sofia | - | AC Milan | 0:2 (0:1) | ||
| 2nd (2nd leg) | AC Milan | - | Vitosha Sofia | 5:2 (3:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 06/10/1988 | Winner: AC Milan | ||||
