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| 1st(1st leg) | Floriana FC | - | Dundee United | 0:0 (0:0) | ||
| 2nd (2nd leg) | Dundee United | - | Floriana FC | 1:0 (0:0) | ||
| 1st(1st leg): 06/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Dundee United | ||||
| 1st(1st leg) | Omonia Nikosia | - | Panathinaikos | 0:1 (0:1) | ||
| 2nd (2nd leg) | Panathinaikos | - | Omonia Nikosia | 2:0 (0:0) | ||
| 1st(1st leg): 06/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Panathinaikos | ||||
| 1st(1st leg) | Grasshopper Club Zürich | - | Eintracht Frankfurt | 0:0 (0:0) | ||
| 2nd (2nd leg) | Eintracht Frankfurt | - | Grasshopper Club Zürich | 1:0 (1:0) | ||
| 1st(1st leg): 06/09/1988 19:30 | 2nd (2nd leg): 04/10/1988 | Winner: Eintracht Frankfurt | ||||
| 1st(1st leg) | KV Mechelen | - | Avenir Beggen | 5:0 (0:0) | ||
| 2nd (2nd leg) | Avenir Beggen | - | KV Mechelen | 1:3 (0:1) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 28/09/1988 | Winner: KV Mechelen | ||||
| 1st(1st leg) | Fram Reykjavík | - | FC Barcelona | 0:2 (0:1) | ||
| 2nd (2nd leg) | FC Barcelona | - | Fram Reykjavík | 5:0 (2:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: FC Barcelona | ||||
| 1st(1st leg) | Dinamo Bucureşti | - | FC Kuusysi (old) | 3:0 (1:0) | ||
| 2nd (2nd leg) | FC Kuusysi (old) | - | Dinamo Bucureşti | 0:3 (0:2) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Dinamo Bucureşti | ||||
| 1st(1st leg) | FC Metz | - | RSC Anderlecht | 1:3 (0:2) | ||
| 2nd (2nd leg) | RSC Anderlecht | - | FC Metz | 2:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: RSC Anderlecht | ||||
| 1st(1st leg) | Glenavon FC | - | Aarhus GF | 1:4 (1:1) | ||
| 2nd (2nd leg) | Aarhus GF | - | Glenavon FC | 3:1 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Aarhus GF | ||||
| 1st(1st leg) | Flamurtari Vlorë | - | Lech Poznań | 2:3 (1:1) | ||
| 2nd (2nd leg) | Lech Poznań | - | Flamurtari Vlorë | 1:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Lech Poznań | ||||
| 1st(1st leg) | FC Carl Zeiss Jena | - | Kremser SC | 5:0 (1:0) | ||
| 2nd (2nd leg) | Kremser SC | - | FC Carl Zeiss Jena | 1:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: FC Carl Zeiss Jena | ||||
| 1st(1st leg) | Derry City | - | Cardiff City | 0:0 (0:0) | ||
| 2nd (2nd leg) | Cardiff City | - | Derry City | 4:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Cardiff City | ||||
| 1st(1st leg) | Borac Banja Luka | - | Metalist Kharkiv | 2:0 (1:0) | ||
| 2nd (2nd leg) | Metalist Kharkiv | - | Borac Banja Luka | 4:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Metalist Kharkiv | ||||
| 1st(1st leg) | Roda JC Kerkrade | - | Vitória Guimarães | 2:0 (0:0) | ||
| 2nd (2nd leg) | Vitória Guimarães | - | Roda JC Kerkrade | 1:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Roda JC Kerkrade | ||||
| 1st(1st leg) | TJ Inter Slovnaft ZŤS Petržalka | - | CFKA Sofia | 2:3 (1:2) | ||
| 2nd (2nd leg) | CFKA Sofia | - | TJ Inter Slovnaft ZŤS Petržalka | 5:0 (5:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: CFKA Sofia | ||||
| 1st(1st leg) | Sakaryaspor | - | Békéscsabai Előre Spartacus SC | 2:0 (1:0) | ||
| 2nd (2nd leg) | Békéscsabai Előre Spartacus SC | - | Sakaryaspor | 1:0 (0:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 05/10/1988 | Winner: Sakaryaspor | ||||
| 1st(1st leg) | IFK Norrköping | - | Sampdoria | 2:1 (1:0) | ||
| 2nd (2nd leg) | Sampdoria | - | IFK Norrköping | 2:0 (1:0) | ||
| 1st(1st leg): 07/09/1988 | 2nd (2nd leg): 06/10/1988 | Winner: Sampdoria | ||||
