Third Round
- Matches played 15–16 July and 22 July
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Celta de Vigo | 5–1 | FK Pelister | 3–0 | 2–1 |
| AaB | 2–3 | Udinese | 0–2 | 2–1 |
| CS Sedan Ardennes | 1–2 | VfL Wolfsburg | 0–0 | 1–2 |
| FK Marila Příbram | 1–3 | Aston Villa F.C. | 0–0 | 1–3 |
| FK Chmel Blšany | 8–0 | Kalamata FC | 5–0 | 3–0 |
| RC Lens | 2–2(a) | VfB Stuttgart | 2–1 | 0–1 |
| Bradford City A.F.C. | 3–0 | RKC Waalwijk | 2–0 | 1–0 |
| FC Rostselmash | 1–5 | AJ Auxerre | 0–2 | 1–3 |
| NK Slaven Belupo | 1–2 | Sigma Olomouc | 1–1 | 0–1 |
| Standard Liège | 4–2 | SV Austria Salzburg | 3–1 | 1–1 |
| Ceahlăul Piatra Neamţ | 2–5 | Austria Wien | 2–2 | 0–3 |
| FC Zenit Saint Petersburg | 4–2 | Tatabánya FC | 2–1 | 2–1 |
Read more about this topic: 2000 UEFA Intertoto Cup
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