| Jeudi 13 & 27 août 1998 |
| RUDAR VELENJE (SLV) - FC Constructorul Chisinau (MOL) | 2-0 0-0 |
| FC Vaduz (LIE) - HELSINBORG IF (SUE) | 0-2 0-3 |
| LAUSANNE SPORTS (SUI) - FC Tsement (ARM) | 5-1 2-1 |
| Cork City (EIRE) - CSKA KIEV (UKR) | 2-1 0-2 |
| Ekranas Panevezys (LIT) - FC APOLLON LIMASSOL (CHY) | 1-2 3-3 |
| Apolonia Fier (ALB) - RC GENK (BEL) | 1-5 0-4 |
| Bangor City (GAL) - HAKA VALKEAKOSKA (FIN) | 0-2 0-1 |
| LEVSKI SOFIA (BUL) - Lokomotiv 96 Vitebsk (BIE) | 8-1 1-1 |
| METALOURG LIEPAJA (LET) - IBK Keflavik (ISL) | 4-2 0-1 |
| CS Grevenmacher (LUX) - RAPID BUCAREST (ROU) | 2-6 0-2 |
| FC Lantana Tallinn (EST) - HEART OF MIDLOTHIAN (ECO) | 0-1 0-5 |
| AMICA WRONKI (POL) - Hibernians La Valette (MAL) | 4-0 1-0 |
| Gi Gotu Itrottarfelag (FER) - MTK BUDAPEST (HON) | 1-3 0-7 |
| Glentoran Belfast (ILN) - MACCABI HAÏFA (ISR) | 0-1 1-2 |
| FC Vardar Skopje (MAC) - SPARTAK TRNAVA (SLQ) | 0-1 0-2 |
| FC COPENHAGUE (DAN) - Karabakh Agdam (AZE) | 6-0 4-0 |
| PARTIZAN BELGRADE (YOU) - Dynamo Batoum (GEO) | 2-0 0-1 |
| Jeudi 17 septembre & 1er octobre 1998 |
| Paris SG (FRA) - MACCABI HAÏFA (ISR) | 1-1 2-3 |
| Rudar Velenje (SLV) - FC VARTEKS VARAZDIN (CRO) | 0-1 0-1 |
| PANIONIOS ATHÈNES (GRE) - Haka Valkeakoska (FIN) | 2-0 3-1 |
| SV RIED (AUT) - MTK Budapest (HON) | 2-0 1-0 |
| Levski Sofia (BUL) - FC COPENHAGUE (DAN) | 0-2 1-4 |
| SC HEERENVEEN (PB) - Amica Wronki (POL) | 3-1 1-0 |
| Heart of Midlothian (ECO) - REAL MAJORQUE (ESP) | 0-1 1-1 |
| CHELSEA FC (ANG) - Helsinborg IF (SUE) | 1-0 0-0 |
| MSV Duisbourg (ALL) - RC GENK (BEL) | 1-1 0-5 |
| BESIKTAS ISTANBUL (TUR) - Spartak Trnava (SLQ) | 3-0 1-2 |
| Rapid Bucarest (ROU) - VALERENGEN IF (NOR) | 2-2 0-0 |
| FC APOLLON LIMASSOL (CHY) - FK Jablonec (RT) | 2-1 1-2 (4-3 tab) |
| Newcastle United (ANG) - PARTIZAN BELGRADE (YOU) | 2-1 0-1 |
| SS LAZIO ROME (ITA) - Lausanne Sports (SUI) | 1-1 2-2 |
| Metalourg Liepaja (LET) - SC BRAGA (POR) | 0-0 0-4 |
| CSKA Kiev (UKR) - LOKOMOTIV MOSCOU (RUS) | 0-2 1-3 |
