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| 1st(1st leg) | Panionios GSS | - | Apollon Limassol | 3:2 (2:2) | ||
| 2nd (2nd leg) | Apollon Limassol | - | Panionios GSS | 0:1 (0:1) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Panionios GSS | ||||
| 1st(1st leg) | Lokomotiv Moskva | - | Sporting Braga | 3:1 (2:0) | ||
| 2nd (2nd leg) | Sporting Braga | - | Lokomotiv Moskva | 1:0 (1:0) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Lokomotiv Moskva | ||||
| 1st(1st leg) | SV Ried | - | Maccabi Haifa | 2:1 (1:1) | ||
| 2nd (2nd leg) | Maccabi Haifa | - | SV Ried | 4:1 (1:0) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Maccabi Haifa | ||||
| 1st(1st leg) | sc Heerenveen | - | NK Varteks | 2:1 (0:0) | ||
| 2nd (2nd leg) | NK Varteks | - | sc Heerenveen | 4:2 (0:1, 2:1) aet | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: NK Varteks | ||||
| 1st(1st leg) | Vålerenga IF | - | Beşiktaş | 1:0 (0:0) | ||
| 2nd (2nd leg) | Beşiktaş | - | Vålerenga IF | 3:3 (3:0) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Vålerenga IF | ||||
| 1st(1st leg) | KRC Genk | - | RCD Mallorca | 1:1 (0:0) | ||
| 2nd (2nd leg) | RCD Mallorca | - | KRC Genk | 0:0 (0:0) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: RCD Mallorca | ||||
| 1st(1st leg) | Lazio Roma | - | Partizan | 0:0 (0:0) | ||
| 2nd (2nd leg) | Partizan | - | Lazio Roma | 2:3 (1:1) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Lazio Roma | ||||
| 1st(1st leg) | Chelsea FC | - | FC København | 1:1 (0:0) | ||
| 2nd (2nd leg) | FC København | - | Chelsea FC | 0:1 (0:1) | ||
| 1st(1st leg): 22/10/1998 | 2nd (2nd leg): 05/11/1998 | Winner: Chelsea FC | ||||
