List of Participants in UEFA Cup Winners' Cup 1998-1999 (49 clubs)
| Club | Country | Participant as.. | M | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|---|
| KS Apolonia Fier |  ALB | 2 | 0 | 0 | 2 | 1 | 9 | -8 | |
| FC Tsement Ararat |  ARM | Domestic cup (winner) | 2 | 0 | 0 | 2 | 2 | 7 | -5 |
| SV Ried |  AUT | Domestic cup (winner) | 4 | 3 | 0 | 1 | 6 | 5 | +1 |
| FK Karabag Agdam |  AZE | 2 | 0 | 0 | 2 | 0 | 10 | -10 | |
| Lokomotiv-96 Vitebsk |  BLR | Domestic cup (winner) | 2 | 0 | 1 | 1 | 2 | 9 | -7 |
| Racing Genk |  BEL | Domestic cup (winner) | 6 | 3 | 3 | 0 | 16 | 3 | +13 |
| Levski Sofia |  BUL | 4 | 1 | 1 | 2 | 10 | 8 | +2 | |
| NK Varteks |  CRO | Domestic cup (runner-up) | 6 | 3 | 1 | 2 | 8 | 7 | +1 |
| Apollon Limassol |  CYP | Domestic cup (runner-up) | 6 | 2 | 1 | 3 | 10 | 11 | -1 |
| FK Jablonec 97 |  CZE | 2 | 1 | 0 | 1 | 3 | 3 | ±0 | |
| FC Copenhagen |  DEN | Domestic cup (runner-up) | 6 | 4 | 1 | 1 | 17 | 3 | +14 |
| Newcastle United |  ENG | Domestic cup (runner-up) | 2 | 1 | 0 | 1 | 2 | 2 | ±0 |
| Chelsea FC | ENG | Defending champion | 8 | 4 | 3 | 1 | 10 | 5 | +5 |
| FC Lantana Tallinn |  EST | Domestic cup (runner-up) | 2 | 0 | 0 | 2 | 0 | 6 | -6 |
| GI Gota |  FAR | 2 | 0 | 0 | 2 | 1 | 10 | -9 | |
| FC Haka |  FIN | 4 | 2 | 0 | 2 | 4 | 5 | -1 | |
| Paris Saint-Germain |  FRA | Domestic cup (winner) | 2 | 0 | 1 | 1 | 3 | 4 | -1 |
| Vardar |  MKD | 2 | 0 | 0 | 2 | 0 | 3 | -3 | |
| FC Dinamo Batumi |  GEO | 2 | 1 | 0 | 1 | 1 | 2 | -1 | |
| MSV Duisburg |  GER | Domestic cup (runner-up) | 2 | 0 | 1 | 1 | 1 | 6 | -5 |
| Panionios |  GRE | Domestic cup (winner) | 6 | 4 | 0 | 2 | 9 | 10 | -1 |
| MTK Budapest |  HUN | 4 | 2 | 0 | 2 | 10 | 4 | +6 | |
| Keflavik IF |  ISL | 2 | 1 | 0 | 1 | 3 | 4 | -1 | |
| Cork City |  IRL | 2 | 1 | 0 | 1 | 2 | 3 | -1 | |
| Maccabi Haifa |  ISR | 8 | 4 | 1 | 3 | 12 | 11 | +1 | |
| SS Lazio |  ITA | Domestic cup (winner) | 9 | 4 | 5 | 0 | 16 | 7 | +9 |
| FK Liepajas Metalurgs |  LAT | Domestic cup (runner-up) | 4 | 1 | 1 | 2 | 4 | 7 | -3 |
| FC Vaduz |  LIE | 2 | 0 | 0 | 2 | 0 | 5 | -5 | |
| Ekranas Panevezys |  LTU | Domestic cup (winner) | 2 | 0 | 1 | 1 | 4 | 5 | -1 |
| CS Grevenmacher |  LUX | Domestic cup (winner) | 2 | 0 | 0 | 2 | 2 | 8 | -6 |
| Hibernians |  MLT | Domestic cup (winner) | 2 | 0 | 0 | 2 | 0 | 5 | -5 |
| Constructorul Chisinau |  MDA | Domestic cup (runner-up) | 2 | 0 | 1 | 1 | 0 | 2 | -2 |
| SC Heerenveen |  NED | Domestic cup (semi-final) | 4 | 3 | 0 | 1 | 8 | 6 | +2 |
| Glentoran |  NIR | 2 | 0 | 0 | 2 | 1 | 3 | -2 | |
| Velerenga IF |  NOR | Domestic cup (winner) | 6 | 1 | 3 | 2 | 8 | 11 | -3 |
| Amika Wronki |  POL | 4 | 2 | 0 | 2 | 6 | 4 | +2 | |
| Sporting de Braga |  POR | Domestic cup (runner-up) | 4 | 2 | 1 | 1 | 6 | 3 | +3 |
| FC Rapid Bucuresti |  ROM | Domestic cup (winner) | 4 | 2 | 2 | 0 | 10 | 4 | +6 |
| Lokomotiv Moscow |  RU | Domestic cup (runner-up) | 8 | 5 | 2 | 1 | 13 | 4 | +9 |
| Heart of Midlothian |  SCO | Domestic cup (winner) | 4 | 2 | 1 | 1 | 7 | 2 | +5 |
| Spartak Trnava |  SVK | 4 | 3 | 0 | 1 | 5 | 4 | +1 | |
| Rudar Velenje |  SLO | 4 | 1 | 1 | 2 | 2 | 2 | ±0 | |
| RCD Mallorca |  ESP | Domestic cup (runner-up) | 9 | 3 | 5 | 1 | 9 | 6 | +3 |
| Helsingborgs IF |  SWE | Domestic cup (winner) | 4 | 2 | 1 | 1 | 5 | 1 | +4 |
| Lausanne Sports |  SUI | Domestic cup (winner) | 4 | 2 | 2 | 0 | 10 | 5 | +5 |
| Besiktas |  TUR | Domestic cup (winner) | 4 | 1 | 1 | 2 | 7 | 6 | +1 |
| CSKA Kyiv |  UA | Domestic cup (runner-up) | 4 | 1 | 0 | 3 | 4 | 7 | -3 |
| Bangor City |  WAL | Domestic cup (winner) | 2 | 0 | 0 | 2 | 0 | 3 | -3 |
| Partizan Belgrade |  YUG | 6 | 2 | 1 | 3 | 6 | 6 | ±0 |
1997/1998
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