Second Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| K.V.C. Westerlo | 0–3 | FC Tescoma Zlín | 0–0 | 0–3 |
| Hibernian F.C. | 1–2 | FK Vėtra | 1–1 | 0–1 |
| K.R.C. Genk | 5–1 | PFC Marek Dupnitsa | 2–1 | 3–0 |
| Odense BK | 0–5 | Villarreal CF | 0–3 | 0–2 |
| FK Teplice | 1–4 | FC Shinnik Yaroslavl | 1–2 | 0–2 |
| FK ZTS Dubnica | 1–7 | FC Slovan Liberec | 1–2 | 0–5 |
| VfL Wolfsburg | 3–7 | FC Thun | 2–3 | 1–4 |
| OFK Beograd | 5–1 | Dinaburg FC | 3–1 | 2–0 |
| NEC Nijmegen | 0–1 | Cork City F.C. | 0–0 | 0–1 |
| Esbjerg fB | 2–1 | OGC Nice | 1–0 | 1–1 |
| FC Spartak Moscow | 5–1 | NK Kamen Ingrad | 4–1 | 1–0 |
| Tampere United | 3–1 | FK Xazar Universiteti Baki | 3–0 | 0–1 |
| Dinamo Minsk | 4–3 | Sartid Smederevo | 1–2 | 3–1(aet) |
| FC Spartak Trnava | 3–1 | FK Sloboda Tuzla | 2–1 | 1–0 |
| FK Vardar | (p)1–1 | K.A.A. Gent | 1–0 | 0–1 |
| NK Slaven Belupo | 2–1 | Vllaznia | 2–0 | 0–1 |
Read more about this topic: 2004 UEFA Intertoto Cup
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