| Tuesday 6th September 1988 | |||
| 1st Leg | |||
| Floriana | 0-0 | Dundee United | |
| Grasshoppers | 0-0 | Eintracht Frankfurt | |
| Omonia Nicosia | 0-1 | Panathinaikos | |
| Wednesday 7th September 1988 | |||
| 1st Leg | |||
| Borac Banja Luka | 2-0 | Metalist Kharkiv | |
| Carl Zeiss Jena | 5-0 | Krems | |
| Derry City | 0-0 | Cardiff City | |
| Dinamo Bucharest | 3-0 | Kuusysi Lahti | |
| Flamurtari Vlore | 2-3 | Lech Poznan | |
| Fram Reykjavik | 0-2 | Barcelona | |
| Glenavon | 1-4 | AGF Aarhus | |
| Inter Bratislava | 2-3 | CFKA Sredets Sofia | |
| Mechelen | 5-0 | Avenir Beggen | |
| Metz | 1-3 | Anderlecht | |
| Norrkoping | 2-1 | Sampdoria | |
| Roda JC | 2-0 | Vitoria Guimaraes | |
| Sakaryaspor | 2-0 | Bekescsaba | |
| 2nd Leg | |||
| Krems | 1-0 | Carl Zeiss Jena | (1-5) |
| Wednesday 28th September 1988 | |||
| 2nd Leg | |||
| Avenir Beggen | 1-3 | Mechelen | (1-8) |
| Tuesday 4th October 1988 | |||
| 2nd Leg | |||
| Eintracht Frankfurt | 1-0 | Grasshoppers | (1-0) |
| Wednesday 5th October 1988 | |||
| 2nd Leg | |||
| AGF Aarhus | 3-1 | Glenavon | (7-2) |
| Anderlecht | 2-0 | Metz | (5-1) |
| Barcelona | 5-0 | Fram Reykjavik | (7-0) |
| Bekescsaba | 1-0 | Sakaryaspor | (1-2) |
| Cardiff City | 4-0 | Derry City | (4-0) |
| CFKA Sredets Sofia | 5-0 | Inter Bratislava | (8-2) |
| Dundee United | 1-0 | Floriana | (1-0) |
| Kuusysi Lahti | 0-3 | Dinamo Bucharest | (0-6) |
| Lech Poznan | 1-0 | Flamurtari Vlore | (4-2) |
| Metalist Kharkiv | 4-0 | Borac Banja Luka | (4-2) |
| Panathinaikos | 2-0 | Omonia Nicosia | (3-0) |
| Vitoria Guimaraes | 1-0 | Roda JC | (1-2) |
| Thursday 6th October 1988 | |||
| 2nd Leg | |||
| Sampdoria | 2-0 | Norrkoping | (3-2) |
