Second Round
- Matches played 1–2 July and 8–9 July
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| FC Nistru Otaci | 3–7 | SV Austria Salzburg | 2–6 | 1–1 |
| FC Zenit Saint Petersburg | 6–1 | NK Primorje | 3–0 | 3–1 |
| Perugia | 2–3 | Standard Liège | 1–2 | 1–1 |
| Nea Salamis FC | 1–3 | Austria Wien | 1–0 | 0–3 |
| Stabæk | 0–5 | AJ Auxerre | 0–2 | 0–3 |
| Dinaburg FC | 0–1 | AaB | 0–0 | 0–1 |
| LASK Linz | 3–4 | FK Marila Příbram | 1–1 | 2–3 |
| FK Atlantas | 2–7 | Bradford City A.F.C. | 1–3 | 1–4 |
| RCD Mallorca | 3–4 | Ceahlăul Piatra Neamţ | 2–1 | 1–3 |
| FK Chmel Blšany | 8–2 | FC Dnepr-Transmash | 6–2 | 2–0 |
| CS Sedan Ardennes | 6–2 | Leiftur | 3–0 | 3–2 |
| Neuchâtel Xamax | 2–10 | VfB Stuttgart | 1–6 | 1–4 |
| Zagłębie Lubin | 1–1(a) | NK Slaven Belupo | 1–1 | 0–0 |
| Tatabánya FC | 3–2 | HNK Cibalia | 3–2 | 0–0 |
| FK Pelister | 3–1 | Västra Frölunda IF | 3–1 | 0–0 |
| Velbazhd Kyustendil | 2–8 | Sigma Olomouc | 2–0 | 0–8 |
Read more about this topic: 2000 UEFA Intertoto Cup
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—Joyce Carol Oates (b. 1938)