The third round of the 2000–01 UEFA Cup began on 21 November 2000. The round included 24 winners from the second round as well as 8 third placed teams from the Champions League First group stage.
| Seeded teams | Group | Unseeded teams | ||
|---|---|---|---|---|
| Team | Coefficient rating | Team | Coefficient rating | |
| 103.799 | 1 | 43.433 | ||
| 56.562 | 32.525 | |||
| 48.201 | 32.250 | |||
| 46.201 | 8.062 | |||
| 79.964 | 2 | 42.201 | ||
| 60.333 | 32.201 | |||
| 51.050 | 29.799 | |||
| 46.364 | 14.500 | |||
| 78.964 | 3 | 43.201 | ||
| 64.364 | 29.201 | |||
| 53.799 | 24.433 | |||
| 52.333 | 15.583 | |||
| 65.964 | 4 | 45.433 | ||
| 61.275 | 34.799 | |||
| 49.728 | 14.562 | |||
| 48.638 | 29.799 | |||
|}
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Internazionale win 2–1 on aggregate.----Parma win 4–2 on aggregate.----Stuttgart win 4–3 on aggregate.----Rayo Vallecano win 2–0 on aggregate.----PSV Eindhoven win 4–0 on aggregate.----Roma win 4–0 on aggregate.----Nantes win 7–4 on aggregate.----Bordeaux win 4–1 on aggregate.----
Liverpool win 4–2 on aggregate.----AEK Athens win 6–4 on aggregate.----Celta Vigo win 1–0 on aggregate.----Alavés win 4–2 on aggregate.----Porto win 2–0 on aggregate.----Slavia Prague win 5–3 on aggregate.----Barcelona win 3–1 on aggregate.----Kaiserslautern win 3–1 on aggregate.