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| 1st(1st leg) | VfB Stuttgart | - | Tatabanya Banyasz SC | 2:0 (0:0) | ||
| 2nd (2nd leg) | Tatabanya Banyasz SC | - | VfB Stuttgart | 2:1 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 11/10/1988 | Winner: VfB Stuttgart | ||||
| 1st(1st leg) | Royal Antwerp FC | - | 1. FC Köln | 2:4 (2:1) | ||
| 2nd (2nd leg) | 1. FC Köln | - | Royal Antwerp FC | 2:1 (2:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 12/10/1988 | Winner: 1. FC Köln | ||||
| 1st(1st leg) | Bayern München | - | Legia Warszawa | 3:1 (2:0) | ||
| 2nd (2nd leg) | Legia Warszawa | - | Bayern München | 3:7 (1:4) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Bayern München | ||||
| 1st(1st leg) | Bayer Leverkusen | - | Os Belenenses | 0:1 (0:0) | ||
| 2nd (2nd leg) | Os Belenenses | - | Bayer Leverkusen | 1:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 12/10/1988 | Winner: Os Belenenses | ||||
| 1st(1st leg) | AS Roma | - | 1. FC Nürnberg | 1:2 (0:1) | ||
| 2nd (2nd leg) | 1. FC Nürnberg | - | AS Roma | 1:3 (1:2, 1:2) aet | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 12/10/1988 | Winner: AS Roma | ||||
| 1st(1st leg) | FC Groningen | - | Atlético Madrid | 1:0 (1:0) | ||
| 2nd (2nd leg) | Atlético Madrid | - | FC Groningen | 2:1 (1:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: FC Groningen | ||||
| 1st(1st leg) | FC Aarau | - | 1. FC Lokomotive Leipzig | 0:3 (0:0) | ||
| 2nd (2nd leg) | 1. FC Lokomotive Leipzig | - | FC Aarau | 4:0 (2:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: 1. FC Lokomotive Leipzig | ||||
| 1st(1st leg) | St Patrick's Athletic | - | Heart of Midlothian | 0:2 (0:2) | ||
| 2nd (2nd leg) | Heart of Midlothian | - | St Patrick's Athletic | 2:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Heart of Midlothian | ||||
| 1st(1st leg) | Zalgiris Vilna | - | Austria Wien | 2:0 (0:0) | ||
| 2nd (2nd leg) | Austria Wien | - | Zalgiris Vilna | 5:2 (4:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Austria Wien | ||||
| 1st(1st leg) | Sporting CP | - | AFC Ajax | 4:2 (3:1) | ||
| 2nd (2nd leg) | AFC Ajax | - | Sporting CP | 1:2 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Sporting CP | ||||
| 1st(1st leg) | Real Sociedad | - | ASVS Dukla Praha | 2:1 (1:1) | ||
| 2nd (2nd leg) | ASVS Dukla Praha | - | Real Sociedad | 3:2 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Real Sociedad | ||||
| 1st(1st leg) | Union Luxembourg | - | RFC Liège | 1:7 (1:2) | ||
| 2nd (2nd leg) | RFC Liège | - | Union Luxembourg | 4:0 (2:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: RFC Liège | ||||
| 1st(1st leg) | Inter | - | IK Brage | 2:1 (1:0) | ||
| 2nd (2nd leg) | IK Brage | - | Inter | 1:2 (1:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Inter | ||||
| 1st(1st leg) | ÍA Akranes | - | Újpesti Dózsa SC | 0:0 (0:0) | ||
| 2nd (2nd leg) | Újpesti Dózsa SC | - | ÍA Akranes | 2:1 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Újpesti Dózsa SC | ||||
| 1st(1st leg) | Rangers FC | - | GKS Katowice | 1:0 (0:0) | ||
| 2nd (2nd leg) | GKS Katowice | - | Rangers FC | 2:4 (1:2) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Rangers FC | ||||
| 1st(1st leg) | Aberdeen FC | - | Dynamo Dresden | 0:0 (0:0) | ||
| 2nd (2nd leg) | Dynamo Dresden | - | Aberdeen FC | 2:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Dynamo Dresden | ||||
| 1st(1st leg) | Dnepr Dnepropetrovsk | - | Girondins Bordeaux | 1:1 (0:1) | ||
| 2nd (2nd leg) | Girondins Bordeaux | - | Dnepr Dnepropetrovsk | 2:1 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Girondins Bordeaux | ||||
| 1st(1st leg) | Östers IF | - | FC DAC 1904 | 2:0 (0:0) | ||
| 2nd (2nd leg) | FC DAC 1904 | - | Östers IF | 6:0 (4:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: FC DAC 1904 | ||||
| 1st(1st leg) | TPS Turku | - | Linfield FC | 0:0 (0:0) | ||
| 2nd (2nd leg) | Linfield FC | - | TPS Turku | 1:1 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: TPS Turku | ||||
| 1st(1st leg) | Molde FK | - | KSV Waregem | 0:0 (0:0) | ||
| 2nd (2nd leg) | KSV Waregem | - | Molde FK | 5:1 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: KSV Waregem | ||||
| 1st(1st leg) | Malmö FF | - | Torpedo Moskva | 2:0 (1:0) | ||
| 2nd (2nd leg) | Torpedo Moskva | - | Malmö FF | 2:1 (1:0, 2:0) aet | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Malmö FF | ||||
| 1st(1st leg) | First Vienna FC | - | Ikast FS | 1:0 (1:0) | ||
| 2nd (2nd leg) | Ikast FS | - | First Vienna FC | 2:1 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: First Vienna FC | ||||
| 1st(1st leg) | Oţelul Galaţi | - | Juventus | 1:0 (0:0) | ||
| 2nd (2nd leg) | Juventus | - | Oţelul Galaţi | 5:0 (3:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Juventus | ||||
| 1st(1st leg) | Velež Mostar | - | APOEL Nikosia | 1:0 (1:0) | ||
| 2nd (2nd leg) | APOEL Nikosia | - | Velež Mostar | 2:5 (1:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Velež Mostar | ||||
| 1st(1st leg) | AEK Athen | - | Athletic Bilbao | 1:0 (1:0) | ||
| 2nd (2nd leg) | Athletic Bilbao | - | AEK Athen | 2:0 (2:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Athletic Bilbao | ||||
| 1st(1st leg) | Montpellier La Paillade SC | - | SL Benfica | 0:3 (0:2) | ||
| 2nd (2nd leg) | SL Benfica | - | Montpellier La Paillade SC | 3:1 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: SL Benfica | ||||
| 1st(1st leg) | Sliema Wanderers | - | Victoria Bucuresti | 0:2 (0:1) | ||
| 2nd (2nd leg) | Victoria Bucuresti | - | Sliema Wanderers | 6:1 (5:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Victoria Bucuresti | ||||
| 1st(1st leg) | SSC Napoli | - | PAOK Saloniki | 1:0 (0:0) | ||
| 2nd (2nd leg) | PAOK Saloniki | - | SSC Napoli | 1:1 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: SSC Napoli | ||||
| 1st(1st leg) | Partizan | - | Slavia Sofia | 5:0 (2:0) | ||
| 2nd (2nd leg) | Slavia Sofia | - | Partizan | 0:5 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Partizan | ||||
| 1st(1st leg) | Servette FC | - | Sturm Graz | 1:0 (0:0) | ||
| 2nd (2nd leg) | Sturm Graz | - | Servette FC | 0:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Servette FC | ||||
| 1st(1st leg) | Trakia Plovdiv | - | Dinamo Minsk | 1:2 (0:1) | ||
| 2nd (2nd leg) | Dinamo Minsk | - | Trakia Plovdiv | 0:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Dinamo Minsk | ||||
| 1st(1st leg) | Beşiktaş | - | Dinamo Zagreb | 1:0 (1:0) | ||
| 2nd (2nd leg) | Dinamo Zagreb | - | Beşiktaş | 2:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Dinamo Zagreb | ||||
