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 |  Celta Vigo | 2–2 | 0–2 | 
| Udinese  | 2–1 |  Legia Warsaw | 1–0 | 1–1 | 
| Deportivo La Coruña  | 5–1 |  Montpellier | 3–1 | 2–0 | 
| Widzew Łódź  | 1–3 |  Monaco | 1–1 | 0–2 | 
| MTK Hungária  | 2–2 (a) |  AEK Athens | 2–1 | 0–1 | 
| Roda  | 0–1 |  Wolfsburg | 0–0 | 0–1 | 
| Anderlecht .svg.png.webp) | 2–4 |  Bologna | 2–1 | 0–3 | 
| PAOK  | 3–3 (1–4 p) |  Benfica | 1–2 | 2–1 (a.e.t.) | 
| Inter Bratislava  | 0–7 |  Nantes | 0–3 | 0–4 | 
| Atlético Madrid  | 5–1 |  Amica Wronki | 1–0 | 4–1 | 
| Parma  | 4–1 |  Helsingborg | 1–0 | 3–1 | 
| Grazer AK  | 2–2 (a) |  Panathinaikos | 2–1 | 0–1 | 
| Steaua București  | 2–0 |  West Ham United | 2–0 | 0–0 | 
| Levski Sofia  | 2–4 |  Juventus | 1–3 | 1–1 | 
| Leeds United  | 7–1 |  Lokomotiv Moscow | 4–1 | 3–0 | 
| Hapoel Haifa  | 1–3 |  Ajax | 0–3 | 1–0 | 
| Slavia Prague  | 3–2 | .svg.png.webp) Grasshopper | 3–1 | 0–1 | 
| Zürich .svg.png.webp) | 2–5 |  Newcastle United | 1–2 | 1–3 | 
| Werder Bremen  | 2–2 (a) |  Viking | 0–0 | 2–2 | 
| Teplice  | 1–5 |  Mallorca | 1–2 | 0–3 | 
| IFK Göteborg  | 0–3 |  Roma | 0–2 | 0–1 | 
| Lyon  | 2–0 |  Celtic | 1–0 | 1–0 | 
| Lens  | 5–2 |  Vitesse | 4–1 | 1–1 | 
| Tottenham Hotspur  | 1–2 |  Kaiserslautern | 1–0 | 0–2 | 
First leg
| Aris  | 2–2 |  Celta Vigo | 
|---|---|---|
| Paulo Andrioli  44' Kyzeridis  68' | Report | Karpin  41', 42' | 
| Deportivo La Coruña  | 3–1 |  Montpellier | 
|---|---|---|
| Pauleta  17' Djalminha  51' (pen.) Makaay  53' | Report | Delaye  6' | 
| Udinese  | 1–0 |  Legia Warsaw | 
|---|---|---|
| Sosa  29' | Report | 
| Slavia Prague  | 3–1 | .svg.png.webp) Grasshopper | 
|---|---|---|
| Ulich  19', 50' Kuchař  40' | Report | Yakin  23' | 
| Widzew Łódź  | 1–1 |  Monaco | 
|---|---|---|
| Wichniarek  5' (pen.) | Report | Giuly  40' | 
| IFK Göteborg  | 0–2 |  Roma | 
|---|---|---|
| Report | Montella  37', 52' | 
| Steaua București  | 2–0 |  West Ham United | 
|---|---|---|
| Rosu  39' Ilie  56' | Report | 
| Anderlecht .svg.png.webp) | 2–1 |  Bologna | 
|---|---|---|
| Koller  17', 35' | Report | Signori  90' | 
| MTK Budapest  | 2–1 |  AEK Athens | 
|---|---|---|
| Egressy  20' Erős  34' | Report | Ćirić  66' | 
| PAOK  | 1–2 |  Benfica | 
|---|---|---|
| Frantzeskos  90' | Report | Nuno Gomes  68' Ronaldo Guiaro  90' | 
| Grazer AK  | 2–1 |  Panathinaikos | 
|---|---|---|
| Lipa  57' Pamić  80' | Report | Sypniewski  64' | 
| Leeds United  | 4–1 |  Lokomotiv Moscow | 
|---|---|---|
| Bowyer  27', 45' Smith  56' Kewell  83' | Report | Loskov  80' | 
| Parma  | 1–0 |  Helsingborg | 
|---|---|---|
| F. Cannavaro  44' | Report | 
| Tottenham Hotspur  | 1–0 |  Kaiserslautern | 
|---|---|---|
| Iversen  33' | Report | 
| Atlético Madrid  | 1–0 |  Amica Wronki | 
|---|---|---|
| Baraja  79' | Report | 
Second leg
| AEK Athens  | 1–0 |  MTK Budapest | 
|---|---|---|
| Ćirić  75' (pen.) | 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 |  Udinese | 
|---|---|---|
| Czereszewski  11' | Report | Sosa  41' | 
Udinese won 2–1 on aggregate.
| Monaco  | 2–0 |  Widzew Łódź | 
|---|---|---|
| Lamouchi  50' Trezeguet  84' | Report | 
Monaco won 3–1 on aggregate.
| Montpellier  | 0–2 |  Deportivo La Coruña | 
|---|---|---|
| Report | Makaay  45' Pauleta  82' | 
Deportivo La Coruña won 5–1 on aggregate.
| Roma  | 1–0 |  IFK Göteborg | 
|---|---|---|
| Fábio Júnior  88' | Report | 
Roma won 3–0 on aggregate.
2–2 on aggregate; Werder Bremen won on away goals.
| Grasshopper .svg.png.webp) | 1–0 |  Slavia Prague | 
|---|---|---|
| Yakin  76' | Report | 
Slavia Prague won 3–2 on aggregate.
| Helsingborg  | 1–3 |  Parma | 
|---|---|---|
| Stavrum  86' | Report | Di Vaio  11', 42', 43' | 
Parma won 4–1 on aggregate.
| Lokomotiv Moscow  | 0–3 |  Leeds United | 
|---|---|---|
| Report | Harte  15' Bridges  28', 45' | 
Leeds United won 7–1 on aggregate.
| Amica Wronki  | 1–4 |  Atlético Madrid | 
|---|---|---|
| Jackiewicz  34' | Report | Hasselbaink  31' Capdevila  45' Baraja  52' Correa  84' | 
Atlético Madrid won 5–1 on aggregate.
| Nantes  | 4–0 |  Inter Bratislava | 
|---|---|---|
| Sibierski  49' Monterrubio  61' Devineau  74' Da Rocha  82' | Report | 
Nantes won 7–0 on aggregate.
| Panathinaikos  | 1–0 |  Grazer AK | 
|---|---|---|
| Pflipsen  90' | Report | 
2–2 on aggregate; Panathinaikos won away goals.
Lens won 5–2 on aggregate.
| Ajax  | 0–1 |  Hapoel Haifa | 
|---|---|---|
| Report | Roso  60' | 
Ajax won 3–1 on aggregate.
| Benfica  | 1–2 (a.e.t.) |  PAOK | 
|---|---|---|
| Kandaurov  50' | Report | Marangos  28' Sabry  44' | 
| Penalties | ||
| Ronaldo Guiaro  Maniche  Chano  Paulo Madeira  | 4–1 |  Frousos  Machairidis  Bandović | 
3–3 on aggregate; Benfica won 4–1 on penalties.
| Kaiserslautern  | 2–0 |  Tottenham Hotspur | 
|---|---|---|
| Buck  89' Carr  90' (o.g.) | Report | 
Kaiserslautern won 2–1 on aggregate.
Lyon won 2–0 on aggregate.
| Juventus  | 1–1 |  Levski Sofia | 
|---|---|---|
| Kovačević  79' | Report | Atanasov  15' | 
Juventus won 4–2 on aggregate.
Newcastle United won 5–2 on aggregate.
Steaua București won 2–0 on aggregate.
| Celta Vigo  | 2–0 |  Aris | 
|---|---|---|
| Đorović  67' Turdó  90' | Report | 
Celta Vigo won 4–2 on aggregate.
Mallorca won 5–1 on aggregate.