Third Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| FC Tobol | 0–4 | SV Pasching | 0–1 | 0–3 |
| Perugia Calcio | 4–0 | AC Allianssi | 2–0 | 2–0 |
| Egaleo FC | 4–5 | FC Koper | 2–3 | 2–2 |
| FC Nantes Atlantique | 5–3 | FC Wil | 2–1 | 3–2 |
| OGC Nice | 0–1 | Werder Bremen | 0–0 | 0–1 |
| Villarreal CF | 3–1 | Brescia Calcio | 2–0 | 1–1 |
| En Avant Guingamp | 4–5 | 1. FC Brno | 2–1 | 2–4(aet) |
| FC Dacia Chişinău | 1–3 | FC Schalke 04 | 0–1 | 1–2 |
| Racing de Santander | 1–3 | FC Slovan Liberec | 0–1 | 1–2 |
| 1. FC Slovácko | 0–3 | VfL Wolfsburg | 0–1 | 0–2 |
| Tampere United | 1–2 | HNK Cibalia | 0–2 | 1–0 |
| sc Heerenveen | 5–1 | Lierse S.K. | 4–1 | 1–0 |
Read more about this topic: 2003 UEFA Intertoto Cup
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