| Thursday 22nd October 1998 | |||
| 1st Leg | |||
| Chelsea | 1-1 | FC Copenhagen | |
| Genk | 1-1 | Mallorca | (n) |
| Heerenveen | 2-1 | Varteks Varazdin | |
| Lazio | 0-0 | Partizan Belgrade | |
| Lokomotiv Moscow | 3-1 | Sporting Braga | |
| Panionios | 3-2 | Apollon Limassol | |
| Ried | 2-1 | Maccabi Haifa | (n) |
| Valerenga | 1-0 | Besiktas | |
| Thursday 5th November 1998 | |||
| 2nd Leg | |||
| Apollon Limassol | 0-1 | Panionios | (2-4) |
| Besiktas | 3-3 | Valerenga | (3-4) |
| FC Copenhagen | 0-1 | Chelsea | (1-2) |
| Maccabi Haifa | 4-1 | Ried | (5-3) |
| Mallorca | 0-0 | Genk | (1-1) |
| (Mallorca won on away goals) | |||
| Partizan Belgrade | 2-3 | Lazio | (2-3) |
| Sporting Braga | 1-0 | Lokomotiv Moscow | (2-3) |
| Varteks Varazdin | 4-2 | Heerenveen | aet (5-4) |









