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| 1st(1st leg) | Bayern München | - | Inter | 0:2 (0:0) | ||
| 2nd (2nd leg) | Inter | - | Bayern München | 1:3 (1:3) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Bayern München | ||||
| 1st(1st leg) | Real Sociedad | - | 1. FC Köln | 1:0 (0:0) | ||
| 2nd (2nd leg) | 1. FC Köln | - | Real Sociedad | 2:2 (2:1) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Real Sociedad | ||||
| 1st(1st leg) | FC Groningen | - | VfB Stuttgart | 1:3 (0:3) | ||
| 2nd (2nd leg) | VfB Stuttgart | - | FC Groningen | 2:0 (1:0) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: VfB Stuttgart | ||||
| 1st(1st leg) | Heart of Midlothian | - | Velež Mostar | 3:0 (1:0) | ||
| 2nd (2nd leg) | Velež Mostar | - | Heart of Midlothian | 2:1 (1:0) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Heart of Midlothian | ||||
| 1st(1st leg) | Girondins Bordeaux | - | SSC Napoli | 0:1 (0:1) | ||
| 2nd (2nd leg) | SSC Napoli | - | Girondins Bordeaux | 0:0 (0:0) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: SSC Napoli | ||||
| 1st(1st leg) | Dynamo Dresden | - | AS Roma | 2:0 (1:0) | ||
| 2nd (2nd leg) | AS Roma | - | Dynamo Dresden | 0:2 (0:0) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Dynamo Dresden | ||||
| 1st(1st leg) | RFC Liège | - | Juventus | 0:1 (0:1) | ||
| 2nd (2nd leg) | Juventus | - | RFC Liège | 1:0 (1:0) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Juventus | ||||
| 1st(1st leg) | Victoria Bucuresti | - | TPS Turku | 1:0 (1:0) | ||
| 2nd (2nd leg) | TPS Turku | - | Victoria Bucuresti | 3:2 (1:2) | ||
| 1st(1st leg): 23/11/1988 | 2nd (2nd leg): 07/12/1988 | Winner: Victoria Bucuresti | ||||
