| Thursday 13th August 1998 | |||
| 1st Leg | |||
| Amica Wronki | 4-0 | Hibernians | |
| Apolonia Fier | 1-5 | Genk | (n) |
| Bangor City | 0-2 | FC Haka Valkeakoski | |
| Cork City | 2-1 | Arsenal Kiev | |
| FC Copenhagen | 6-0 | FK Qarabag | |
| FC Vaduz | 0-2 | Helsingborgs | |
| FK Ekranas Panevezys | 1-2 | Apollon Limassol | |
| FK Vardar Skopje | 0-1 | Spartak Trnava | |
| Glentoran | 0-1 | Maccabi Haifa | |
| Grevenmacher | 2-6 | Rapid Bucharest | (n) |
| Lantana Tallinn | 0-1 | Heart of Midlothian | |
| Lausanne-Sports | 5-1 | Tsement Ararat | |
| Levski Sofia | 8-1 | Lokomotiv-96 Vitebsk | |
| Metalurgs Liepajas | 4-2 | Keflavik | |
| NK Rudar Velenje | 2-0 | Constructorul Chisin | |
| Partizan Belgrade | 2-0 | Dinamo Batumi | |
| Vikingur Gota | 1-3 | MTK Budapest | (n) |
| Thursday 27th August 1998 | |||
| 2nd Leg | |||
| Apollon Limassol | 3-3 | FK Ekranas Panevezys | (5-4) |
| Arsenal Kiev | 2-0 | Cork City | (3-2) |
| Constructorul Chisin | 0-0 | NK Rudar Velenje | (0-2) |
| Dinamo Batumi | 1-1 | Partizan Belgrade | (1-3) |
| FC Haka Valkeakoski | 1-0 | Bangor City | (3-0) |
| FK Qarabag | 0-4 | FC Copenhagen | (n) (0-10) |
| Genk | 4-0 | Apolonia Fier | (9-1) |
| Heart of Midlothian | 5-0 | Lantana Tallinn | (6-0) |
| Helsingborgs | 3-0 | FC Vaduz | (5-0) |
| Hibernians | 0-1 | Amica Wronki | (0-5) |
| Keflavik | 1-0 | Metalurgs Liepajas | (3-4) |
| Lokomotiv-96 Vitebsk | 1-1 | Levski Sofia | (2-9) |
| Maccabi Haifa | 2-1 | Glentoran | (3-1) |
| MTK Budapest | 7-0 | Vikingur Gota | (10-1) |
| Rapid Bucharest | 2-0 | Grevenmacher | (8-2) |
| Spartak Trnava | 2-0 | FK Vardar Skopje | (3-0) |
| Tsement Ararat | 1-2 | Lausanne-Sports | (n) (2-7) |
