The third round of the 1999–2000 UEFA Cup began on 23 November 1999. The round included 24 winners from the second round and eight third-placed teams from the Champions League first group stage.
Matches
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg | 
|---|---|---|---|---|
| Ajax  | 0–3 |  Mallorca | 0–1 | 0–2 | 
| AEK Athens  | 2–3 |  Monaco | 2–2 | 0–1 | 
| Rangers  | 2–2 (1–3 p) |  Borussia Dortmund | 2–0 | 0–2 (a.e.t.) | 
| Bologna  | 2–3 |  Galatasaray | 1–1 | 1–2 | 
| Roma  | 1–0 |  Newcastle United | 1–0 | 0–0 | 
| Spartak Moscow  | 2–2 (a) |  Leeds United | 2–1 | 0–1 | 
| Slavia Prague  | 5–2 |  Steaua București | 4–1 | 1–1 | 
| Udinese  | 2–2 (a) |  Bayer Leverkusen | 0–1 | 2–1 | 
| Arsenal  | 6–3 |  Nantes | 3–0 | 3–3 | 
| Deportivo La Coruña  | 5–3 |  Panathinaikos | 4–2 | 1–1 | 
| Parma  | 5–4 |  Sturm Graz | 2–1 | 3–3 (a.e.t.) | 
| Lyon  | 3–4 |  Werder Bremen | 3–0 | 0–4 | 
| Olympiacos  | 3–4 |  Juventus | 1–3 | 2–1 | 
| Celta Vigo  | 8–1 |  Benfica | 7–0 | 1–1 | 
| Wolfsburg  | 3–5 |  Atlético Madrid | 2–3 | 1–2 | 
| Lens  | 5–3 |  Kaiserslautern | 1–2 | 4–1 | 
First leg
| Udinese  | 0–1 |  Bayer Leverkusen | 
|---|---|---|
| Report | Ballack  76' | 
| AEK Athens  | 2–2 |  Monaco | 
|---|---|---|
| Nikolaidis  45', 89' | Report | Giuly  26' Simone  78' | 
| Bologna  | 1–1 |  Galatasaray | 
|---|---|---|
| Signori  66' | Report | Şükür  81' | 
| Slavia Prague  | 4–1 |  Steaua București | 
|---|---|---|
| Dostálek  1', 47' Horváth  35' Došek  56' | Report | Luţu  82' | 
| Lens  | 1–2 |  Kaiserslautern | 
|---|---|---|
| Schjønberg  85' (o.g.) | Report | Sikora  32' (o.g.) Wagner  38' | 
| Wolfsburg  | 2–3 |  Atlético Madrid | 
|---|---|---|
| Juskowiak  21' Akonnor  83' (pen.) | Report | Aguilera  6', 58' Hasselbaink  37' | 
| Olympiacos  | 1–3 |  Juventus | 
|---|---|---|
| Giannakopoulos  15' | Report | Tudor  27' Kovačević  67' Inzaghi  88' | 
| Lyon  | 3–0 |  Werder Bremen | 
|---|---|---|
| Anderson  13', 45' Vairelles  77' | Report | 
| Deportivo La Coruña  | 4–2 |  Panathinaikos | 
|---|---|---|
| Olivares  7' (o.g.) Pauleta  11' Djalminha  13' Donato  30' | Report | Warzycha  29' Galetto  66' | 
| Roma  | 1–0 |  Newcastle United | 
|---|---|---|
| Totti  50' (pen.) | Report | 
| Celta Vigo  | 7–0 |  Benfica | 
|---|---|---|
| Karpin  16' (pen.), 54' Makélélé  30' Turdó  39', 50' Juanfran  42' Mostovoi  61' | Report | 
| Spartak Moscow  | 2–1 |  Leeds United | 
|---|---|---|
| Shirko  38' Róbson  65' | Report | Kewell  14' | 
Second leg
| Borussia Dortmund  | 2–0 (a.e.t.) |  Rangers | 
|---|---|---|
| Ikpeba  28' Bobic  90' | Report | |
| Penalties | ||
| Bobic  Nijhuis  Nerlinger  Barbarez  | 3–1 |  Amoruso  van Bronckhorst  Numan  Reyna | 
Borussia Dortmund 2–2 Rangers on aggregate. Borussia Dortmund won 3–1 on penalties.
Juventus won 4–3 on aggregate.
Werder Bremen won 4–3 on aggregate.
Galatasaray won 3–2 on aggregate.
Lens won 5–3 on aggregate.
Parma won 5–4 on aggregate.
| Steaua București  | 1–1 |  Slavia Prague | 
|---|---|---|
| Ciocoiu  45' | Report | Dostálek  50' | 
Slavia Prague won 5–2 on aggregate.
| Monaco  | 1–0 |  AEK Athens | 
|---|---|---|
| Simone  32' | Report | 
AS Monaco won 3–2 on aggregate.
| Panathinaikos  | 1–1 |  Deportivo La Coruña | 
|---|---|---|
| Asanović  78' (pen.) | Report | Makaay  90' | 
Deportivo La Coruña won 5–3 on aggregate.
| Bayer Leverkusen  | 1–2 |  Udinese | 
|---|---|---|
| Ballack  22' | Report | Margiotta  9', 18' | 
Bayer Leverkusen 2–2 Udinese on aggregate. Udinese won on away goals rule.
Arsenal won 6–3 on aggregate.
| Leeds United  | 1–0 |  Spartak Moscow | 
|---|---|---|
| Radebe  84' | Report | 
Leeds United 2–2 Spartak Moscow on aggregate. Leeds United won on away goals rule.
Roma won 1–0 on aggregate.
Celta Vigo won 8–1 on aggregate.
| Atlético Madrid  | 2–1 |  Wolfsburg | 
|---|---|---|
| Hasselbaink  4' Correa  86' | Report | Akonnor  56' (pen.) | 
Atlético Madrid won 5–3 on aggregate.
Mallorca won 3–0 on aggregate.