| Aris (Greece) vs Servette (Switzerland) |
| Inter Bratislava (Slovakia) vs Rapid Wien (Austria) |
| Omonia (Cyprus) vs Juventus (Italy) |
| Crvena Zvezda (Yugoslavia) vs Montpellier (France) |
| Ajax Amsterdam (Netherlands) vs Dukla Banská Bystrica (Slovakia) |
| Partizan (Yugoslavia) vs Leeds United (England) |
| Bodř/Glimt (Norway) vs Werder Bremen (Germany) |
| Helsingborgs IF (Sweden) vs Karpaty Lviv (Ukraine) |
| Lausanne-Sports (Switzerland) vs Celta Vigo (Spain) |
| Skonto (Latvia) vs Widzew Lódz (Poland) |
| Parma (Italy) vs Kryvbas Kryvyi Rig (Ukraine) |
| Wolfsburg (Germany) vs Debreceni VSC |
| Teplice (Czech Republic) vs Ferencvárosi (Hungary) |
| Tottenham Hotspur (England) vs Zimbru Chisinau (Moldova) |
| Atlético Madrid (Spain) vs Ankaragücü (Turkey) |
| Maccabi Tel-Aviv (Israel) vs Lens (France |
| Beira Mar (Portugal) vs Vitesse Arnhem (Netherlands) |
| Monaco (France) vs St. Johnstone (Scotland) |
| Torpedo Kutaisi (Georgia) vs AEK (Greece) |
| West Ham United (England) vs Osijek (Croatia) |
| Lokomotiv Tbilisi (Georgia) vs PAOK (Greece) |
| Amica Wronki (Poland) vs Brřndby (Denmark) |
| Roma (Italy) vs Vitória (Portugal) |
| Anderlecht (Belgium) vs Olimpija Ljubljana (Slovenia) |
| Lech Poznán (Poland) vs IFK Göteborg (Sweden) |
| Celtic (Scotland) vs Hapoel Tel-Aviv (Israel) |
| HJK (Finland) vs Olympique Lyonnais (France) |
| Sigma Olomouc (Czech Republic) vs Real Mallorca (Spain) |
| Grasshopper (Switzerland) vs AB (Denmark) |
| CSKA Sofia (Bulgaria) vs Newcastle United (England) |
| Dinamo Bucuresti (Romania) vs Benfica (Portugal) |
| MTK (Hungary) vs Fenerbahçe (Turkey) |
| Viking (Norway) vs Sporting (Portugal |
| Grazer AK (Austria) vs Spartak Trnava (Slovakia) |
| Ionikos (Greece) vs Nantes (France) |
| Hapoel Haifa (Israel) vs Club Brugge (Belgium) |
| Anorthosis Famagusta (Cyprus) vs Legia Warszawa (Poland) |
| NK Gorica (Slovenia) vs Panathinaikos (Greece) |
| Steaua Bucuresti (Romania) vs LASK (Austria) |
| Zenit (Russia) vs Bologna (Italy) |
| Roda (Netherlands) vs Shakhtar Donetsk (Ukraine) |
| Kaiserslautern (Germany) vs Kilmarnock (Scotland) |
| Levski Sofia (Bulgaria) vs Hajduk Split (Croatia) |
| Lokomotiv Moscow (Russia) vs Lyngby (Denmark) |
| Vojvodina (Yugoslavia) vs Slavia Praha (Czech Republic) |
| FC Zürich (Switzerland) vs Lierse (Belgium) |
| Stabćk (Norway) vs Deportivo (Spain) |
| Udinese (Italy) vs Aalborg (Denmark) |
1999-2000 UEFA Cup Draw
