The first round of the 1999–2000 UEFA Cup began on 14 September 1999. The round included 38 winners from the qualifying round, 16 losing teams from the Champions League 3rd qualifying round, 3 winners of the Intertoto Cup and 39 new entrants. This narrowed the clubs from 96, down to 48 teams in preparation for the second round.
Seeding
| Group 1 | Group 2 | Group 3 | Group 4 | ||||
|---|---|---|---|---|---|---|---|
| Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | 
| Group 5 | Group 6 | Group 7 | Group 8 | ||||
| Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | 
| 
 
  | 
|||||||
| Group 9 | Group 10 | Group 11 | Group 12 | ||||
| Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | Seeded | Unseeded | 
Summary
Matches
| Steaua București  | 2–0 | |
|---|---|---|
| Ciocoiu  Dănciulescu  | 
Report | 
Steaua București won 5–2 on aggregate.
Wolfsburg won 3–2 on aggregate.
| Red Star Belgrade  | 0–1 | |
|---|---|---|
| Report | Loko  | 
| Montpellier  | 2–2 | |
|---|---|---|
| Ouédec  Delaye  | 
Report | Jelić  Bošković  | 
Montpellier won 3–2 on aggregate.
| Stabæk  | 1–0 | |
|---|---|---|
| Finstad  | 
Report | 
| Deportivo La Coruña  | 2–0 | |
|---|---|---|
| Jokanović  Conceição  | 
Report | 
Deportivo La Coruña won 2–1 on aggregate.
Udinese won 3–1 on aggregate.
| Leeds United  | 1–0 | |
|---|---|---|
| Huckerby  | 
Report | 
Leeds United won 4–1 on aggregate.
| HJK Helsinki  | 0–1 | |
|---|---|---|
| Report | Vairelles  | 
Lyon won 6–1 on aggregate.
| Atlético Madrid  | 3–0 | |
|---|---|---|
| Gamarra  Hasselbaink Paunović  | 
Report | 
| Ankaragücü  | 1–0 | |
|---|---|---|
| Aksancak  | 
Report | 
Atlético Madrid won 3–1 on aggregate.
| Fenerbahçe  | 0–2 | |
|---|---|---|
| Report | Kenesei  | 
MTK Hungária won 2–0 on aggregate.
| Anderlecht  | 3–1 | |
|---|---|---|
| Bajrektarevič  Radzinski  | 
Report | Ekmečič  | 
| Olimpija Ljubljana  | 0–3 | |
|---|---|---|
| Report | Koller  Radzinski  | 
Anderlecht won 6–1 on aggregate.
| Roda JC  | 2–0 | |
|---|---|---|
| Doomernik  Zafarin  | 
Report | 
| Shakhtar Donetsk  | 1–3 | |
|---|---|---|
| Benyo  | 
Report | Tchoutang  van der Luer van Dessel  | 
Roda JC won 5–1 on aggregate.
| Bodø/Glimt  | 0–5 | |
|---|---|---|
| Report | Pizarro  Bogdanović Maksymov  | 
| Werder Bremen  | 1–1 | |
|---|---|---|
| Aílton  | 
Report | Staurvik  | 
Werder Bremen won 6–1 on aggregate.
| Sporting CP  | 1–0 | |
|---|---|---|
| Ayew  | 
Report | 
Viking won 3–1 on aggregate.
Lens won 4–3 on aggregate.
| Kaiserslautern  | 3–0 | |
|---|---|---|
| Koch  Djorkaeff Marschall  | 
Report | 
| Kilmarnock  | 0–2 | |
|---|---|---|
| Report | Djorkaeff  Ramzy  | 
Kilmarnock won 5–0 on aggregate.
| Helsingborg  | 1–1 | |
|---|---|---|
| Jonson  | 
Report | Hetsko  | 
| Karpaty Lviv  | 1–1 | |
|---|---|---|
| Hetsko  | 
Report | Jonson  | 
| Penalties | ||
| Hetsko  Yevtushok Mizin Pavliukh  | 
2–4 | |
2–2 on aggregate; Helsingborg won 4–2 on penalties.
| Lech Poznań  | 1–2 | |
|---|---|---|
| Żurawski  | 
Report | Andersson  Mild  | 
IFK Göteborg won 2–1 on aggregate.
| Teplice  | 3–1 | |
|---|---|---|
| Frýdek  Kolomazník Rízek  | 
Report | Tóth  | 
Teplice won 4–2 on aggregate.
| CSKA Sofia  | 0–2 | |
|---|---|---|
| Report | Solano  Ketsbaia  | 
| Newcastle United  | 2–2 | |
|---|---|---|
| Shearer  Robinson  | 
Report | Litera  Simeonov  | 
Newcastle United won 4–2 on aggregate.
| Gorica  | 0–1 | |
|---|---|---|
| Report | Liberopoulos  | 
| Panathinaikos  | 2–0 | |
|---|---|---|
| Sigurðsson  Nasiopoulos  | 
Report | 
Panathinaikos won 3–0 on aggregate.
| Amica Wronki  | 2–0 | |
|---|---|---|
| Dawidowski  Bosacki  | 
Report | 
| Brøndby  | 4–3 | |
|---|---|---|
| Madsen  Vragel Christensen  | 
Report | Kryszałowicz  Kukiełka  | 
Amica Wronki won 5–4 on aggregate.
Vitesse won 2–0 on aggregate.
Grazer AK won 4–2 on aggregate.
| Levski Sofia  | 3–0 | |
|---|---|---|
| Ivankov  Bachev Dimitrov  | 
Report | 
Levski Sofia won 3–0 on aggregate.
| Celtic  | 2–0 | |
|---|---|---|
| Larsson  | 
Report | 
| Hapoel Tel Aviv  | 0–1 | |
|---|---|---|
| Report | Larsson  | 
Celtic won 3–0 on aggregate.
| Lausanne-Sports  | 3–2 | |
|---|---|---|
| Kuzba  Mazzoni  | 
Report | Revivo  Karpin  | 
| Celta Vigo  | 4–0 | |
|---|---|---|
| McCarthy  Mostovoi  | 
Report | 
Celta Vigo won 6–3 on aggregate.
| Ionikos  | 1–3 | |
|---|---|---|
  | 
Report | 
  | 
Nantes won 4–1 on aggregate.
Aris won 3–2 on aggregate.
| Monaco  | 3–0 | |
|---|---|---|
| Simone  Trezeguet  | 
Report | 
| St Johnstone  | 3–3 | |
|---|---|---|
| Griffin  Dasovic O'Neil  | 
Report | Léonard  Pršo Legwinski  | 
Monaco won 6–3 on aggregate.
| Inter Bratislava  | 1–0 | |
|---|---|---|
| Ľalík  | 
Report | 
| Rapid Wien  | 1–2 | |
|---|---|---|
| Zingler  | 
Report | Suchancok  Babnič  | 
Inter Bratislava won 3–1 on aggregate.
| Lokomotiv Moscow  | 3–0 | |
|---|---|---|
| Kharlachev  Drozdov Janashia  | 
Report | 
Lokomotiv Moscow won 5–1 on aggregate.
| Skonto  | 1–0 | |
|---|---|---|
| Astafjevs  | 
Report | 
| Widzew Łódź  | 2–0 | |
|---|---|---|
| Wichniarek  Gęsior  | 
Report | 
Widzew Łódź won 2–1 on aggregate.
| Roma  | 7–0 | |
|---|---|---|
| Aldair  Montella Alenichev Assunção Delvecchio  | 
Report | 
| Vitória de Setúbal  | 1–0 | |
|---|---|---|
| Makinwa  | 
Report | 
Roma won 7–1 on aggregate.
| Parma  | 3–2 | |
|---|---|---|
| Di Vaio  Baggio  | 
Report | Palyanytsya  Monaryov  | 
| Kryvbas Kryvyi Rih  | 0–3 | |
|---|---|---|
| Report | Boghossian  Crespo Di Vaio  | 
Parma won 6–2 on aggregate.
| Hapoel Haifa  | 3–1 | |
|---|---|---|
| Turgeman  Sivilia  | 
Report | Jankauskas  | 
| Club Brugge  | 4–2 | |
|---|---|---|
| Verheyen  Borkelmans Janssen  | 
Report | Roso  Turgeman  | 
5-5 on aggregate; Hapoel Haifa won on away goals.
| Torpedo Kutaisi  | 0–1 | |
|---|---|---|
| Report | 
  | 
| AEK Athens  | 6–1 | |
|---|---|---|
| Report | 
  | 
AEK Athens won 7–1 on aggregate.
| Omonia  | 2–5 | |
|---|---|---|
| Kontolefteros  | 
Report | Inzaghi  Kovačević Esnáider Del Piero  | 
Juventus won 10–2 on aggregate.
West Ham United won 6–1 on aggregate.
| Slavia Prague  | 3–2 | |
|---|---|---|
| Petrouš  Došek Zelenka  | 
Report | Belić  Bogdanović  | 
Slavia Prague won 3–2 on aggregate.
Mallorca won 3–1 on aggregate.
| Benfica  | 0–1 | |
|---|---|---|
| Report | Năstase  | 
| Dinamo București  | 0–2 | |
|---|---|---|
| Report | Maniche  Chano  | 
Benfica won 2–1 on aggregate.
| Ajax  | 6–1 | |
|---|---|---|
| Verlaat  Reuser Knopper Machlas Wamberto  | 
Report | Verlaat  | 
| Dukla Banská Bystrica  | 1–3 | |
|---|---|---|
| Malatinský  | 
Report | Arveladze  Bobson Laudrup  | 
Ajax won 9–2 on aggregate.
| Tottenham Hotspur  | 3–0 | |
|---|---|---|
| Leonhardsen  Perry Sherwood  | 
Report | 
Tottenham Hotspur won 3–0 on aggregate.
| Bologna  | 2–2 | |
|---|---|---|
| Fontolan  Cipriani  | 
Report | Panov  Kondrashov  | 
Bologna won 5–2 on aggregate.
| Anorthosis  | 1–0 | |
|---|---|---|
| Engomitis  | 
Report | 
| Legia Warsaw  | 2–0 | |
|---|---|---|
| Mięciel  Czereszewski  | 
Report | 
Legia Warsaw won 2–0 on aggregate.
| Locomotive Tbilisi  | 0–7 | |
|---|---|---|
| Report | Georgiadis  Sabry Frousos Frantzeskos Vryzas  | 
| PAOK  | 2–0 | |
|---|---|---|
| Valencia  Salpingidis  | 
Report | 
PAOK won 9–0 on aggregate.
| AB Copenhagen  | 0–2 | |
|---|---|---|
| Report | Bjur  Ekoku  | 
| Grasshopper  | 1–1 | |
|---|---|---|
| Magro  | 
Report | Daugaard  | 
Grasshopper won 3–1 on aggregate.
| Lierse  | 3–4 | |
|---|---|---|
| Van Meir  Huysegems Zdebel  | 
Report | Jamarauli  Frick Eydelie Daems  | 
Zürich won 5–3 on aggregate.