| Wednesday 22nd July 1998 | |||
| 1st Leg | |||
| Beitar Jerusalem | 4-1 | B36 Torshavn | |
| Celtic | 0-0 | St Patrick's Ath | |
| Cliftonville | 1-5 | Kosice | |
| Dinamo Kiev | 8-0 | Barry Town | |
| Dinamo Tbilisi | 3-0 | Vllaznia Shkoder | |
| (Dinamo Tbilisi awarded match) | |||
| Grasshoppers | 6-0 | Jeunesse Esch | |
| HJK Helsinki | 2-0 | FK Yerevan | |
| Kareda-Sakalas S | 0-3 | Maribor Teatanic | |
| Liteks Lovech | 2-0 | Halmstads | |
| LKS Lodz | 4-1 | Kapaz Ganja | |
| Obilic | 2-0 | IBV Vestmannaeyjar | |
| Sileks Kratovo | 0-0 | Club Brugge | |
| Skonto Riga | 0-0 | Dinamo Minsk | |
| Steaua Bucharest | 4-1 | Flora Tallinn | |
| Valletta | 0-2 | Anorthosis Famagusta | |
| Zimbru Chisinau | 1-0 | Ujpest Dozsa | |
| Monday 27th July 1998 | |||
| 2nd Leg | |||
| B36 Torshavn | 0-1 | Beitar Jerusalem | (1-5) |
| Wednesday 29th July 1998 | |||
| 2nd Leg | |||
| Anorthosis Famagusta | 6-0 | Valletta | (8-0) |
| Barry Town | 1-2 | Dinamo Kiev | (1-10) |
| Club Brugge | 2-1 | Sileks Kratovo | (2-1) |
| Dinamo Minsk | 1-2 | Skonto Riga | (1-2) |
| FK Yerevan | 0-3 | HJK Helsinki | (0-5) |
| Flora Tallinn | 3-1 | Steaua Bucharest | (4-5) |
| Halmstads | 2-1 | Liteks Lovech | (2-3) |
| IBV Vestmannaeyjar | 1-2 | Obilic | (1-4) |
| Jeunesse Esch | 0-2 | Grasshoppers | (0-8) |
| Kapaz Ganja | 1-3 | LKS Lodz | (2-7) |
| Kosice | 8-0 | Cliftonville | (13-1) |
| Maribor Teatanic | 1-0 | Kareda-Sakalas S | (4-0) |
| St Patrick's Ath | 0-2 | Celtic | (0-2) |
| Ujpest Dozsa | 3-1 | Zimbru Chisinau | (3-2) |
| Vllaznia Shkoder | 3-1 | Dinamo Tbilisi | (3-4) |
