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| 1st(1st leg) | CFKA Sofia | - | Panathinaikos | 2:0 (1:0) | ||
| 2nd (2nd leg) | Panathinaikos | - | CFKA Sofia | 0:1 (0:0) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: CFKA Sofia | ||||
| 1st(1st leg) | FC Carl Zeiss Jena | - | Sampdoria | 1:1 (1:0) | ||
| 2nd (2nd leg) | Sampdoria | - | FC Carl Zeiss Jena | 3:1 (2:0) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: Sampdoria | ||||
| 1st(1st leg) | Roda JC Kerkrade | - | Metalist Kharkiv | 1:0 (1:0) | ||
| 2nd (2nd leg) | Metalist Kharkiv | - | Roda JC Kerkrade | 0:0 (0:0) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: Roda JC Kerkrade | ||||
| 1st(1st leg) | FC Barcelona | - | Lech Poznań | 1:1 (1:0) | ||
| 2nd (2nd leg) | Lech Poznań | - | FC Barcelona | 4:5 (1:1, 1:1, 1:1) pso | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: FC Barcelona | ||||
| 1st(1st leg) | KV Mechelen | - | RSC Anderlecht | 1:0 (0:0) | ||
| 2nd (2nd leg) | RSC Anderlecht | - | KV Mechelen | 0:2 (0:1) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: KV Mechelen | ||||
| 1st(1st leg) | Eintracht Frankfurt | - | Sakaryaspor | 3:1 (3:0) | ||
| 2nd (2nd leg) | Sakaryaspor | - | Eintracht Frankfurt | 0:3 (0:2) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: Eintracht Frankfurt | ||||
| 1st(1st leg) | Dundee United | - | Dinamo Bucureşti | 0:1 (0:0) | ||
| 2nd (2nd leg) | Dinamo Bucureşti | - | Dundee United | 1:1 (0:0) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: Dinamo Bucureşti | ||||
| 1st(1st leg) | Cardiff City | - | Aarhus GF | 1:2 (1:1) | ||
| 2nd (2nd leg) | Aarhus GF | - | Cardiff City | 4:0 (2:0) | ||
| 1st(1st leg): 26/10/1988 | 2nd (2nd leg): 09/11/1988 | Winner: Aarhus GF | ||||
