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| 1st(1st leg) | Rudar Velenje | - | NK Varteks | 0:1 (0:0) | ||
| 2nd (2nd leg) | NK Varteks | - | Rudar Velenje | 1:0 (1:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: NK Varteks | ||||
| 1st(1st leg) | Rapid Bucureşti | - | Vålerenga IF | 2:2 (0:0) | ||
| 2nd (2nd leg) | Vålerenga IF | - | Rapid Bucureşti | 0:0 (0:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Vålerenga IF | ||||
| 1st(1st leg) | Panionios GSS | - | Haka Valkeakoski | 2:0 (1:0) | ||
| 2nd (2nd leg) | Haka Valkeakoski | - | Panionios GSS | 1:3 (0:2) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Panionios GSS | ||||
| 1st(1st leg) | Levski Sofia | - | FC København | 0:2 (0:1) | ||
| 2nd (2nd leg) | FC København | - | Levski Sofia | 4:1 (1:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: FC København | ||||
| 1st(1st leg) | SV Ried | - | MTK Hungaria | 2:0 (1:0) | ||
| 2nd (2nd leg) | MTK Hungaria | - | SV Ried | 0:1 (0:1) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: SV Ried | ||||
| 1st(1st leg) | CSKA Kiev | - | Lokomotiv Moskva | 0:2 (0:1) | ||
| 2nd (2nd leg) | Lokomotiv Moskva | - | CSKA Kiev | 3:1 (1:1) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Lokomotiv Moskva | ||||
| 1st(1st leg) | Apollon Limassol | - | FK Jablonec 97 | 2:1 (0:1) | ||
| 2nd (2nd leg) | FK Jablonec 97 | - | Apollon Limassol | 3:4 (2:0, 2:1, 2:1) pso | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Apollon Limassol | ||||
| 1st(1st leg) | FK Liepājas Metalurgs | - | Sporting Braga | 0:0 (0:0) | ||
| 2nd (2nd leg) | Sporting Braga | - | FK Liepājas Metalurgs | 4:0 (2:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Sporting Braga | ||||
| 1st(1st leg) | Beşiktaş | - | Spartak Trnava | 3:0 (2:0) | ||
| 2nd (2nd leg) | Spartak Trnava | - | Beşiktaş | 2:1 (0:1) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Beşiktaş | ||||
| 1st(1st leg) | MSV Duisburg | - | KRC Genk | 1:1 (0:0) | ||
| 2nd (2nd leg) | KRC Genk | - | MSV Duisburg | 5:0 (2:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: KRC Genk | ||||
| 1st(1st leg) | Chelsea FC | - | Helsingborgs IF | 1:0 (1:0) | ||
| 2nd (2nd leg) | Helsingborgs IF | - | Chelsea FC | 0:0 (0:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Chelsea FC | ||||
| 1st(1st leg) | Lazio Roma | - | Lausanne Sports | 1:1 (1:0) | ||
| 2nd (2nd leg) | Lausanne Sports | - | Lazio Roma | 2:2 (1:2) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Lazio Roma | ||||
| 1st(1st leg) | Newcastle United | - | Partizan | 2:1 (1:0) | ||
| 2nd (2nd leg) | Partizan | - | Newcastle United | 1:0 (0:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Partizan | ||||
| 1st(1st leg) | sc Heerenveen | - | Amica Wronki | 3:1 (2:0) | ||
| 2nd (2nd leg) | Amica Wronki | - | sc Heerenveen | 0:1 (0:1) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: sc Heerenveen | ||||
| 1st(1st leg) | Paris Saint-Germain | - | Maccabi Haifa | 1:1 (0:0) | ||
| 2nd (2nd leg) | Maccabi Haifa | - | Paris Saint-Germain | 3:2 (0:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: Maccabi Haifa | ||||
| 1st(1st leg) | Heart of Midlothian | - | RCD Mallorca | 0:1 (0:1) | ||
| 2nd (2nd leg) | RCD Mallorca | - | Heart of Midlothian | 1:1 (0:0) | ||
| 1st(1st leg): 17/09/1998 | 2nd (2nd leg): 01/10/1998 | Winner: RCD Mallorca | ||||
