| UEFA Cup 1999-2000 Seedings | COEFF | OUT | ||
| 1 | ENG | Arsenal FC London | 40.144 | |
| 2 | TUR | Galatasaray SK İstanbul | 31.175 | |
| - | FRA | RC Lens | 36.721 | SF |
| - | ENG | Leeds United FC | 22.144 | SF |
| - | CZE | SK Slavia Praha | 42.812 | QF |
| - | ESP | RCD Mallorca | 38.814 | QF |
| - | ESP | RC Celta Vigo | 36.814 | QF |
| - | GER | SV Werder Bremen | 35.749 | QF |
| - | ITA | Juventus FC Torino | 121.606 | R4 |
| - | ITA | Parma AC | 87.606 | R4 |
| - | GER | BV Borussia 09 Dortmund | 84.749 | R4 |
| - | ESP | C Atlético Madrid | 67.814 | R4 |
| - | FRA | AS Monaco | 63.721 | R4 |
| - | ITA | Roma AS | 56.606 | R4 |
| - | ESP | RCD La Coruña | 43.814 | R4 |
| - | ITA | Udinese C | 33.606 | R4 |
| - | NED | AFC Ajax Amsterdam | 91.908 | R3 |
| - | RUS | OSFK Spartak Moskva | 62.912 | R3 |
| - | GER | TSV Bayer 04 Leverkusen | 54.749 | R3 |
| - | FRA | Olympique Lyonnais | 49.721 | R3 |
| - | POR | SL Benfica Lisboa | 49.358 | R3 |
| - | FRA | FC Nantes Atlantique | 47.721 | R3 |
| - | ITA | Bologna FC | 44.606 | R3 |
| - | GER | 1.FC Kaiserslautern | 43.749 | R3 |
| - | GRE | Panathinaïkos AO Áthina | 41.475 | R3 |
| - | ENG | Newcastle United FC | 39.144 | R3 |
| - | GRE | AEK Áthina | 38.475 | R3 |
| - | GRE | Olympiakós SFP Pireás | 36.475 | R3 |
| - | ROM | CSA Steaua Bucureşti | 31.100 | R3 |
| - | GER | Vfl Wolfsburg | 22.749 | R3 |
| - | SCO | Rangers FC Glasgow | 22.312 | R3 |
| - | AUT | SK Sturm Graz | 21.187 | R3 |
| - | RUS | MFK Lokomotive Moskva | 43.912 | R2 |
| - | NED | Roda JC Kerkrade | 31.908 | R2 |
| - | SUI | Grasshoppers C Zürich | 30.000 | R2 |
| - | SWE | IFK Göteborg | 29.662 | R2 |
| - | BEL | RSC Anderlecht Bruxelles | 26.800 | R2 |
| - | NED | SBV-Vitesse Arnhem | 25.908 | R2 |
| - | FRA | Montpellier HSC | 21.721 | R2 |
| - | POL | Legia Daewoo Warszawa | 20.626 | R2 |
| - | SCO | Celtic FC Glasgow | 19.312 | R2 |
| - | AUT | Grazer AK | 19.187 | R2 |
| - | SUI | FC Zürich | 18.000 | R2 |
| - | GRE | PAOK Thessaloníki | 17.475 | R2 |
| - | ENG | Tottenham Hotspur FC London | 17.144 | R2 |
| - | ENG | West Ham United FC London | 17.144 | R2 |
| - | POL | RTS Widzew-Piast Łódź | 16.625 | R2 |
| - | SWE | Helsingborgs IF | 15.662 | R2 |
| - | GRE | Aris GS Thessaloníki | 15.475 | R2 |
| - | HUN | MTK Hungária FC Budapest | 12.833 | R2 |
| - | CZE | FK Teplice | 11.812 | R2 |
| - | NOR | Viking FK Stavanger | 10.866 | R2 |
| - | POL | KS Amica Wronki | 8.625 | R2 |
| - | SVK | AŠK Inter Slovnaft Bratislava | 7.166 | R2 |
| - | ISR | Hapoel opel Haifa FC | 5.770 | R2 |
| - | BUL | PFK Levski Sofija | 3.791 | R2 |
| - | BEL | Club Brügge KV | 40.800 | R1 |
| - | DEN | Brøndby IF København | 38.525 | R1 |
| - | AUT | SK Rapid Wien | 35.187 | R1 |
| - | POR | Sporting CP Lisboa | 30.358 | R1 |
| - | HUN | Ferencvárosi TC Budapest | 23.833 | R1 |
| - | CRO | HNK Hajduk Split | 20.187 | R1 |
| - | TUR | Fenerbahçe SK İstanbul | 19.175 | R1 |
| - | DEN | AAB Ålborg | 14.525 | R1 |
| - | UKR | FK Shakhtyor Donets'k | 14.145 | R1 |
| - | RUS | FK Zenit Sankt Petersburg | 13.912 | R1 |
| - | GRE | FC Ionikós Níkaia | 13.475 | R1 |
| - | CZE | SK Sigma Olomouc MZ | 12.812 | R1 |
| - | POR | SC Beira Mar Aveiro | 12.358 | R1 |
| - | POR | Vitória FC Setúbal | 12.358 | R1 |
| - | SUI | Lausanne-Sports | 12.000 | R1 |
| - | SUI | Servette FC Genève | 12.000 | R1 |
| - | NOR | SoFK Bodø-Glimt | 11.866 | R1 |
| - | BEL | K Lierse SK | 11.800 | R1 |
| - | DEN | Lyngby BK København | 11.525 | R1 |
| - | AUT | FC LASK Linz | 11.187 | R1 |
| - | DEN | AB Akademisk København | 10.525 | R1 |
| - | FIN | HJK Helsinki | 10.520 | R1 |
| - | SVN | NK SCT Olimpija Ljubljana | 10.415 | R1 |
| - | CRO | NK Osijek | 10.187 | R1 |
| - | TUR | MKE Ankaragücü SK | 10.175 | R1 |
| - | UKR | FK Kryvbas Kryvyj Rih | 10.145 | R1 |
| - | UKR | FK Karpaty L'viv | 10.145 | R1 |
| - | YUG | FK Crvena Zvezda Beograd | 10.124 | R1 |
| - | NOR | Stabæk IF Bekkestua | 9.866 | R1 |
| - | CYP | Anorthosis FC of Ammokhostos Lárnaka | 9.332 | R1 |
| - | SCO | Kilmarnock FC | 9.312 | R1 |
| - | SVK | FC Spartak Trnava | 9.166 | R1 |
| - | ROM | FC Dinamo Bucureşti | 9.100 | R1 |
| - | POL | KKS Lech Poznań | 8.625 | R1 |
| - | SCO | St. Johnstone FC Perth | 8.312 | R1 |
| - | HUN | Debreceni VSC-Epona | 7.833 | R1 |
| - | ISR | Maccabi Visa Tel-Aviv FC | 7.770 | R1 |
| - | SVK | FC Dukla Banská Bystrica | 7.166 | R1 |
| - | YUG | FK Partizan Beograd | 7.124 | R1 |
| - | CYP | Omónoia AC Lefkosía | 6.332 | R1 |
| - | LVA | Skonto FK Riga | 6.291 | R1 |
| - | MDA | FC Zimbru Chişinău | 6.166 | R1 |
| - | GEO | FC Torpedo Kutaisi | 6.083 | R1 |
| - | GEO | FC Lokomotivi Tbilisi | 6.083 | R1 |
| - | BUL | FK CSKA Sofija | 5.791 | R1 |
| - | ISR | Hapoel Tel Aviv FC | 5.770 | R1 |
| - | SVN | NK HIT Gorica | 5.415 | R1 |
| - | YUG | FK Vojvodina Novi Sad | 4.124 | R1 |
| - | HUN | Újpesti TE Budapest | 8.833 | Q |
| - | CYP | Apoel FC Lefkosía | 8.332 | Q |
| - | BLR | FC Belshina Bobruysk | 4.541 | Q |
| - | BLR | FK BATE Barysau | 4.541 | Q |
| - | FIN | VPS Vaasa | 4.520 | Q |
| - | LVA | FK Liepājas Metalurgs | 4.291 | Q |
| - | ISL | KR Reykjavík | 4.166 | Q |
| - | MKD | FK Vardar Skopje | 3.457 | Q |
| - | LVA | Riga FK | 3.291 | Q |
| - | ISL | Leiftur ÍF Olafsfjörđur | 3.166 | Q |
| - | MKD | Sileks FC Kratovo | 2.457 | Q |
| - | LTU | FK Žalgiris Kaunas | 2.416 | Q |
| - | LTU | FK Kareda Šiauliai | 2.416 | Q |
| - | MDA | Constructorul FC Chişinău | 2.166 | Q |
| - | MDA | FC Sheriff Tiraspol | 2.166 | Q |
| - | NIR | Linfield FC Belfast | 1.999 | Q |
| - | EST | FC Lantana Tallinn | 1.291 | Q |
| - | EST | FC Levadia Maardu | 1.291 | Q |
| - | EST | JK Tulevik Viljandi | 1.291 | Q |
| - | ARM | FK Jerevan | 1.208 | Q |
| - | ARM | FK Shirak Gyumri | 1.208 | Q |
| - | NIR | Portadown FC Armagh | 0.999 | Q |
| - | WAL | Cwmbran Town AFC | 0.916 | Q |
| - | WAL | Inter Cable Tel Cardiff FC Bridgend | 0.916 | Q |
| - | IRL | Bray Wanderers FC | 0.916 | Q |
| - | IRL | Cork City FC | 0.916 | Q |
| - | MLT | Birkirkara FC | 0.749 | Q |
| - | MLT | Sliema Wanderers FC | 0.749 | Q |
| - | FRO | B36 Tórshavn | 0.624 | Q |
| - | FRO | KÍ Klakksvík | 0.624 | Q |
| - | ALB | CS Vllaznia Shkodër | 0.583 | Q |
| - | ALB | KS Bylis Ballshi | 0.583 | Q |
| - | LUX | F'91 Dudelange | 0.583 | Q |
| - | LUX | FC Mondercange | 0.583 | Q |
| - | LIE | FC Vaduz | 0.500 | Q |
| - | AZE | Neftchi Bakı FK | 0.458 | Q |
| - | AZE | Shamkir FK | 0.458 | Q |
| - | AND | CE Principat Inter Trade Andorra-La-Vella | 0.000 | Q |