The second round of the 1999–2000 UEFA Cup began on 19 October 1999. The round included 48 winners from the first round.
Matches
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Aris |
2–4 | 2–2 | 0–2 | |
| Udinese |
2–1 | 1–0 | 1–1 | |
| Deportivo La Coruña |
5–1 | 3–1 | 2–0 | |
| Widzew Łódź |
1–3 | 1–1 | 0–2 | |
| MTK Hungária |
2–2 (a) | 2–1 | 0–1 | |
| Roda |
0–1 | 0–0 | 0–1 | |
| Anderlecht |
2–4 | 2–1 | 0–3 | |
| PAOK |
3–3 (1–4 p) | 1–2 | 2–1 (a.e.t.) | |
| Inter Bratislava |
0–7 | 0–3 | 0–4 | |
| Atlético Madrid |
5–1 | 1–0 | 4–1 | |
| Parma |
4–1 | 1–0 | 3–1 | |
| Grazer AK |
2–2 (a) | 2–1 | 0–1 | |
| Steaua București |
2–0 | 2–0 | 0–0 | |
| Levski Sofia |
2–4 | 1–3 | 1–1 | |
| Leeds United |
7–1 | 4–1 | 3–0 | |
| Hapoel Haifa |
1–3 | 0–3 | 1–0 | |
| Slavia Prague |
3–2 | 3–1 | 0–1 | |
| Zürich |
2–5 | 1–2 | 1–3 | |
| Werder Bremen |
2–2 (a) | 0–0 | 2–2 | |
| Teplice |
1–5 | 1–2 | 0–3 | |
| IFK Göteborg |
0–3 | 0–2 | 0–1 | |
| Lyon |
2–0 | 1–0 | 1–0 | |
| Lens |
5–2 | 4–1 | 1–1 | |
| Tottenham Hotspur |
1–2 | 1–0 | 0–2 |
First leg
| Aris | 2–2 | |
|---|---|---|
| Paulo Andrioli Kyzeridis |
Report | Karpin |
| Deportivo La Coruña | 3–1 | |
|---|---|---|
| Pauleta Djalminha Makaay |
Report | Delaye |
| Udinese | 1–0 | |
|---|---|---|
| Sosa |
Report |
| Slavia Prague | 3–1 | |
|---|---|---|
| Ulich Kuchař |
Report | Yakin |
| Widzew Łódź | 1–1 | |
|---|---|---|
| Wichniarek |
Report | Giuly |
| IFK Göteborg | 0–2 | |
|---|---|---|
| Report | Montella |
| Steaua București | 2–0 | |
|---|---|---|
| Rosu Ilie |
Report |
| Anderlecht | 2–1 | |
|---|---|---|
| Koller |
Report | Signori |
| MTK Budapest | 2–1 | |
|---|---|---|
| Egressy Erős |
Report | Ćirić |
| PAOK | 1–2 | |
|---|---|---|
| Frantzeskos |
Report | Nuno Gomes Ronaldo Guiaro |
| Grazer AK | 2–1 | |
|---|---|---|
| Lipa Pamić |
Report | Sypniewski |
| Leeds United | 4–1 | |
|---|---|---|
| Bowyer Smith Kewell |
Report | Loskov |
| Parma | 1–0 | |
|---|---|---|
| F. Cannavaro |
Report |
| Tottenham Hotspur | 1–0 | |
|---|---|---|
| Iversen |
Report |
| Atlético Madrid | 1–0 | |
|---|---|---|
| Baraja |
Report |
Second leg
| AEK Athens | 1–0 | |
|---|---|---|
| Ćirić |
Report |
2–2 on aggregate; AEK Athens won on away goals.
Bologna won 4–2 on aggregate.
Wolfsburg won 1–0 on aggregate.
| Legia Warsaw | 1–1 | |
|---|---|---|
| Czereszewski |
Report | Sosa |
Udinese won 2–1 on aggregate.
| Monaco | 2–0 | |
|---|---|---|
| Lamouchi Trezeguet |
Report |
Monaco won 3–1 on aggregate.
| Montpellier | 0–2 | |
|---|---|---|
| Report | Makaay Pauleta |
Deportivo La Coruña won 5–1 on aggregate.
| Roma | 1–0 | |
|---|---|---|
| Fábio Júnior |
Report |
Roma won 3–0 on aggregate.
2–2 on aggregate; Werder Bremen won on away goals.
| Grasshopper | 1–0 | |
|---|---|---|
| Yakin |
Report |
Slavia Prague won 3–2 on aggregate.
| Helsingborg | 1–3 | |
|---|---|---|
| Stavrum |
Report | Di Vaio |
Parma won 4–1 on aggregate.
| Lokomotiv Moscow | 0–3 | |
|---|---|---|
| Report | Harte Bridges |
Leeds United won 7–1 on aggregate.
| Amica Wronki | 1–4 | |
|---|---|---|
| Jackiewicz |
Report | Hasselbaink Capdevila Baraja Correa |
Atlético Madrid won 5–1 on aggregate.
| Nantes | 4–0 | |
|---|---|---|
| Sibierski Monterrubio Devineau Da Rocha |
Report |
Nantes won 7–0 on aggregate.
| Panathinaikos | 1–0 | |
|---|---|---|
| Pflipsen |
Report |
2–2 on aggregate; Panathinaikos won away goals.
Lens won 5–2 on aggregate.
| Ajax | 0–1 | |
|---|---|---|
| Report | Roso |
Ajax won 3–1 on aggregate.
| Benfica | 1–2 (a.e.t.) | |
|---|---|---|
| Kandaurov |
Report | Marangos Sabry |
| Penalties | ||
| Ronaldo Guiaro Maniche Chano Paulo Madeira |
4–1 | |
3–3 on aggregate; Benfica won 4–1 on penalties.
| Kaiserslautern | 2–0 | |
|---|---|---|
| Buck Carr |
Report |
Kaiserslautern won 2–1 on aggregate.
Lyon won 2–0 on aggregate.
| Juventus | 1–1 | |
|---|---|---|
| Kovačević |
Report | Atanasov |
Juventus won 4–2 on aggregate.
Newcastle United won 5–2 on aggregate.
Steaua București won 2–0 on aggregate.
| Celta Vigo | 2–0 | |
|---|---|---|
| Đorović Turdó |
Report |
Celta Vigo won 4–2 on aggregate.
Mallorca won 5–1 on aggregate.