Second Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Akratitos | 0–1 | AC Allianssi | 0–1 | 0–0 |
| Örgryte IS | 4–4(a) | OGC Nice | 3–2 | 1–2 |
| 1. FC Slovácko | 4–3 | OFK Beograd | 1–0 | 3–3 |
| Racing de Santander | (a)2–2 | Győr ETO FC | 1–0 | 1–2 |
| FC Slovan Liberec | 4–0 | Shamrock Rovers F.C. | 2–0 | 2–0 |
| FC Thun | 3–4 | 1. FC Brno | 2–3 | 1–1 |
| Brescia Calcio | 3–2 | Gloria Bistriţa | 2–1 | 1–1 |
| PFC Marek Dupnitsa | 1–3 | VfL Wolfsburg | 1–1 | 0–2 |
| FC Shakhtyor | 3–5 | HNK Cibalia | 1–1 | 2–4 |
| K. Sint-Truidense V.V. | 0–3 | FC Tobol | 0–2 | 0–1 |
| Willem II Tilburg | 3–4 | FC Wil | 2–1 | 1–3 |
| FK Pobeda | 2–3 | SV Pasching | 1–1 | 1–2 |
| FK Sloboda Tuzla | 2–5 | Lierse S.K. | 1–0 | 1–5 |
| Tampere United | 1–0 | FK Sutjeska | 0–0 | 1–0 |
| FC Dacia Chişinău | 5–0 | KF Partizani Tirana | 2–0 | 3–0 |
| FC Koper | (a)3–3 | FK ZTS Dubnica | 1–0 | 2–3 |
Read more about this topic: 2003 UEFA Intertoto Cup
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