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| Qualifying Round | First Round |
| Second Round | Quarter Finals |
| Semi Finals | Final |
| 1st Leg
13-Aug-98 |
2nd Leg
27-Aug-98 |
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| Rudar Velenje (Slovenia) | Constractorul Chis. (Moldova) | 2 - 0 | 0 - 0 |
| Vaduz (Liechtenstein) | Helsingborg IF (Sweden) | 0 - 2 | 0 - 3 |
| Lausanne (Switzerland) | Tsement Ararat (Armenia) | 5 - 1 | 2 - 1 |
| Cork City (EIRE) | CSKA Kiev (Ukraine) | 2 - 1 | 0 - 2 |
| Ekranas Panevez. (Lithuania) | Apollon Limassol (Cyprus) | 1 - 2 | 3 - 3 |
| Apolonia Fier (Albania) | Racing Genk (Belgium) | 1 - 5 | 0 - 4 |
| Bangor City (Wales) | FC Haka (Finland) | 0 - 2 | 0 - 1 |
| Levski Sofia (Bulgaria) | Lokomotiv-96 (Belarus) | 8 - 1 | 1 - 1 |
| Liepaja Metalurgs (Latvia) | IB Keflavik (Iceland) | 4 - 2 | 0 - 1 |
| Grevenmacher (Luxemburg) | Rapid Bucuresti (Romania) | 2 - 6 | 0 - 2 |
| Lantana (Estonia) | Heart of Midloth. (Scotland) | 0 - 1 | 0 - 5 |
| Amica Wronki (Poland) | Hibernians (Malta) | 4 - 0 | 1 - 0 |
| Gotu Itrottarfelag (Faroe Isl.) | MTK (Hungary) | 1 - 3 | 0 - 7 |
| Glentoran (N. Ireland) | Maccabi Haifa (Israel) | 0 - 1 | 1 - 2 |
| Vardar Skopje (FYROM) | Spartak Trnava (Slovakia) | 0 - 1 | 0 - 2 |
| FC Kobenhavn (Denmark) | Karabakh Agd. (Azerbaijan) | 6 - 0 | 4 - 0 |
| Partizan (Yugoslavia) | Dinamo Batumi (Georgia) | 2 - 0 | 0 - 1 |
| - The teams that go through to the first round are shown in bold. |
| 1st Leg
17-Sep-98 |
2nd Leg
1-Oct-98 |
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| Rudar Velenje (Slovenia) | Varteks Varazdin (Croatia) | 0 - 1 | 0 - 1 |
| Panionios (Greece) | FC Haka (Finland) | 2 - 0 | 3 - 1 |
| SV Ried (Austria) | MTK (Hungary) | 2 - 0 | 1 - 0 |
| Levski Sofia (Bulgaria) | FC Kobenhavn (Denmark) | 0 - 2 | 1 - 4 |
| SC Heerenveen (Netherlands) | Amica Wronki (Poland) | 3 - 1 | 1 - 0 |
| Heart of Midloth. (Scotland) | Real Mallorca (Spain) | 0 - 1 | 1 - 1 |
| Chelsea (England) | Helsingborg IF (Sweden) | 1 - 0 | 0 - 0 |
| MSV Duisburg (Germany) | Racing Genk (Belgium) | 1 - 1 | 0 - 5 |
| Rapid Bucuresti (Romania) | Valerenga (Norway) | 2 - 2 | 0 - 0 |
| Besiktas (Turkey) | Spartak Trnava (Slovakia) | 3 - 0 | 1 - 2 |
| Apollon Limassol (Cyprus) (1) | Jablonec (Czech Rep.) | 2 - 1 | 1 - 2 |
| Newcastle United (England) | Partizan (Yugoslavia) | 2 - 1 | 0 - 1 |
| Lazio (Italy) | Lausanne (Switzerland) | 1 - 1 | 2 - 2 |
| Paris Saint-Germain FC (France) | Maccabi Haifa (Israel) | 1 - 1 | 2 - 3 |
| Liepaja Metalurgs (Latvia) | SC Braga (Portugal) | 0 - 0 | 0 - 4 |
| CSKA Kiev (Ukraine) | Lokomotiv Moscow (Russia) | 0 - 2 | 1 - 3 |
| (1) Apollon Limassol advance to the next round winning the tie 4-3 on penalties. |
| - The teams that go through to the second round are shown in bold. |
| 1st Leg
22-Oct-98 |
2nd Leg
5-Nov-98 |
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| Lazio (Italy) | Partizan (Yugoslavia) | 0 - 0 | 3 - 2 |
| Valerenga (Norway) | Besiktas (Turkey) | 1 - 0 | 3 - 3 |
| SC Heerenveen (Netherlands) | Varteks Varazdin (Croatia) (1) | 2 - 1 | 2 - 4 |
| Racing Genk (Belgium) | Real Mallorca (Spain) | 1 - 1 | 0 - 0 |
| Panionios (Greece) | Apollon Limassol (Cyprus) | 3 - 2 | 1 - 0 |
| SV Ried (Austria) | Maccabi Haifa (Israel) | 2 - 1 | 1 - 4 |
| Lokomotiv Moscow (Russia) | SC Braga (Portugal) | 3 - 1 | 1 - 0 |
| Chelsea (England) | FC Kobenhavn (Denmark) | 1 - 1 | 1 - 0 |
| (1) After extra time. |
| - The teams that go through to the quarter-finals are shown in bold. |
| 1st Leg
4-Mar-99 |
2nd Leg
18-Mar-99 |
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| Chelsea (England) | Valerenga (Norway) | 3 - 0 | 3 - 2 |
| Lokomotiv Moscow (Russia) | Maccabi Haifa (Israel) | 3 - 0 | 1 - 0 |
| Varteks Varazdin (Croatia) | Real Mallorca (Spain) | 0 - 0 | 1 - 3 |
| Panionios (Greece) | Lazio (Italy) | 0 - 4 | 0 - 3 |
| - The teams that go through to the semi-finals are shown in bold. |
| 1st Leg
1-Apr-99 |
2nd Leg
15-Apr-99 |
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| Chelsea (England) | Real Mallorca (Spain) | 1 - 1 | 0 - 1 |
| Lokomotiv Moscow (Russia) | Lazio (Italy) | 1 - 1 | 0 - 0 |
| - The teams that go through to final are shown in bold. |
| 19-May-99 | ||
| Real Mallorca (Spain) | Lazio (Italy) | 1 - 2 |
| - Click on the result for match details. |
| - are the Cup Winners' Cup Winners for 1998-99. |
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