| Wednesday 12th August 1998 | |||
| 1st Leg | |||
| Bayern Munich | 4-0 | Obilic | |
| Benfica | 6-0 | Beitar Jerusalem | |
| Celtic | 1-0 | Croatia Zagreb | |
| Dinamo Kiev | 0-1 | Sparta Prague | |
| Dinamo Tbilisi | 2-1 | Athletic Bilbao | |
| Galatasaray | 2-1 | Grasshoppers | |
| HJK Helsinki | 1-0 | Metz | |
| Inter Milan | 4-0 | Skonto Riga | (n) |
| Kosice | 0-2 | Brondby | |
| Liteks Lovech | 0-5 | Spartak Moscow | (n) |
| Manchester United | 2-0 | LKS Lodz | |
| Maribor Teatanic | 2-1 | PSV Eindhoven | |
| Olympiakos | 2-1 | Anorthosis Famagusta | |
| Rosenborg | 2-0 | Club Brugge | |
| Steaua Bucharest | 2-2 | Panathinaikos | |
| Sturm Graz | 4-0 | Ujpest Dozsa | |
| Wednesday 26th August 1998 | |||
| 2nd Leg | |||
| Anorthosis Famagusta | 2-4 | Olympiakos | (3-6) |
| Athletic Bilbao | 1-0 | Dinamo Tbilisi | (2-2) |
| (Athletic Bilbao won on away goals) | |||
| Beitar Jerusalem | 4-2 | Benfica | (4-8) |
| Brondby | 0-1 | Kosice | (2-1) |
| Club Brugge | 4-2 | Rosenborg | (4-4) |
| (Rosenborg won on away goals) | |||
| Croatia Zagreb | 3-0 | Celtic | (3-1) |
| Grasshoppers | 2-3 | Galatasaray | (3-5) |
| LKS Lodz | 0-0 | Manchester United | (0-2) |
| Metz | 1-1 | HJK Helsinki | (1-2) |
| Obilic | 1-1 | Bayern Munich | (1-5) |
| Panathinaikos | 6-3 | Steaua Bucharest | (8-5) |
| PSV Eindhoven | 4-1 | Maribor Teatanic | aet (5-3) |
| Skonto Riga | 1-3 | Inter Milan | (1-7) |
| Sparta Prague | 0-1 | Dinamo Kiev | aet (1-1) |
| (Dinamo Kiev won on penalties) | |||
| Spartak Moscow | 6-2 | Liteks Lovech | (11-2) |
| Ujpest Dozsa | 2-3 | Sturm Graz | (2-7) |
