- Alon Mizrahi is the top scorer of the tournament
UEFA Cup Winners' Cup 1998/99Qualifying round  | NK Rudar, Velenje | 2:0, 0:0 | FC Constructorul, Chişinău | | FC Vaduz, Vaduz | 0:2, 0:3 | Helsingborgs IF, Helsingborg | | FC Lausanne-Sports, Lausanne | 5:1, 2:1 | Tsement FC, Ararat | | Cork City FC, Cork | 2:1, 0:2 | FC CSKA, Kyiv | | FK Ekranas, Panevėžys | 1:2, 3:3 | AFC Apollon, Limassol | | KF Apolonia, Fier | 1:5, 0:4 | KRC Genk, Genk | | Bangor City FC, Bangor | 0:2, 0:1 | FC Haka, Valkeakoski | | PFC Levski, Sofia | 8:1, 1:1 | FC Lakamatyw 96, Vitebsk | | FHK Liepājas Metalurgs, Liepāja | 4:2, 0:1 | ÍUMFK, Reykjanesbær | | CS Grevenmacher, Gréiwemaacher | 2:6, 0:2 | UFC Rapid, Bucureşti | | FC Lantana/Marlekor, Tallinn | 0:1, 0:5 | Heart of Midlothian FC, Edinburgh | | KS Amica, Wronki | 4:0, 1:0 | Hibernians FC, Raħal Ġdid | | GÍ, Gøta | 1:3, 0:7 | MTK Hungária, Budapest | | Glentoran FC, Belfast | 0:1, 1:2 | Maccabi Haifa FC, Haifa | | FK Vardar, Skopje | 0:1, 0:2 | FC Spartak, Trnava | | FC København, København | 6:0, 4:0 | Qarabağ FK, Ağdam | | FK Partizan, Beograd | 2:0, 0:1 | FC Dinamo, Batumi |
First round | FC CSKA, Kyiv | 0:2, 1:3 | FC Lokomotiv, Moscow | | FHK Liepājas Metalurgs, Liepāja | 0:0, 0:4 | Sporting Clube de Braga, Braga | | SV Ried, Ried im Innkreis | 2:0, 1:0 | MTK Hungária, Budapest | | Paris Saint-Germain FC, Paris | 1:1, 2:3 | Maccabi Haifa FC, Haifa | | Panionios GAS, Nea Smyrni | 2:0, 3:1 | FC Haka, Valkeakoski | | AFC Apollon, Limassol | 2:1, 1:2
(4:3 pen.) | FK Jablonec 97, Jablonec nad Nisou | | SS Lazio SpA, Roma | 1:1, 2:2 | FC Lausanne-Sports, Lausanne | | Newcastle United FC, Newcastle upon Tyne | 2:1, 0:1 | FK Partizan, Beograd | | Chelsea FC, London | 1:0, 0:0 | Helsingborgs IF, Helsingborg | | PFC Levski, Sofia | 0:2, 1:4 | FC København, København | | UFC Rapid, Bucureşti | 2:2, 0:0 | Vålerenga Fotball, Oslo | | Beşiktaş JK, İstanbul | 3:0, 1:2 | FC Spartak, Trnava | | SC Heerenveen, Heerenveen | 3:1, 1:0 | KS Amica, Wronki | | NK Rudar, Velenje | 0:1, 0:1 | NK Varteks, Varaždin | | MSV, Duisburg | 1:1, 0:5 | KRC Genk, Genk | | Heart of Midlothian FC, Edinburgh | 0:1, 1:1 | RCD Mallorca, Palma |
Round of 16 | FC Lokomotiv, Moscow | 3:1, 0:1 | Sporting Clube de Braga, Braga | | SV Ried, Ried im Innkreis | 2:1, 1:4 | Maccabi Haifa FC, Haifa | | Panionios GAS, Nea Smyrni | 3:2, 1:0 | AFC Apollon, Limassol | | SS Lazio SpA, Roma | 0:0, 3:2 | FK Partizan, Beograd | | Chelsea FC, London | 1:1, 1:0 | FC København, København | | Vålerenga Fotball, Oslo | 1:0, 3:3 | Beşiktaş JK, İstanbul | | SC Heerenveen, Heerenveen | 2:1, 2:4 | NK Varteks, Varaždin | | KRC Genk, Genk | 1:1, 0:0 | RCD Mallorca, Palma |
Quarterfinals | FC Lokomotiv, Moscow | 3:0, 1:0 | Maccabi Haifa FC, Haifa | | Panionios GAS, Nea Smyrni | 0:4, 0:3 | SS Lazio SpA, Roma | | Chelsea FC, London | 3:0, 3:2 | Vålerenga Fotball, Oslo | | NK Varteks, Varaždin | 0:0, 1:3 | RCD Mallorca, Palma |
Semifinals Final Top scorers | Player | Club | Goals | | Alon Mizrahi | Maccabi Haifa FC, Haifa | 7 | | Zaza Janashia | FC Lokomotiv, Moscow | 6 | | Souleymane Oulare | KRC Genk, Genk | 5 | | Milenko Špoljarić | AFC Apollon, Limassol | 5 | | Dmitriy Bulykin | FC Lokomotiv, Moscow | 4 | | John Carew | Vålerenga Fotball, Oslo | 4 | | Fabio Celestini | FC Lausanne-Sports, Lausanne | 4 | | Dani García | RCD Mallorca, Palma | 4 | | Krisztián Kenesei | MTK Hungária, Budapest | 4 | | Pavel Nedvěd | SS Lazio SpA, Roma | 4 | | Oktay Derelioğlu | Beşiktaş JK, İstanbul | 4 | | Dejan Stanković | SS Lazio SpA, Roma | 4 | | Branko Strupar | KRC Genk, Genk | 4 |
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