Third Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| FC Tescoma Zlín | 4–4(a) | Atlético Madrid | 2–4 | 2–0 |
| FC Nantes Atlantique | 4–2 | Cork City F.C. | 3–1 | 1–1 |
| K.R.C. Genk | (a)2–2 | Borussia Dortmund | 0–1 | 2–1 |
| FC Thun | 3–5 | Hamburger SV | 2–2 | 1–3 |
| FC Shinnik Yaroslavl | 2–6 | UD Leiria | 1–4 | 1–2 |
| FC Schalke 04 | 7–1 | FK Vardar | 5–0 | 2–1 |
| FC Slovan Liberec | 2–1 | Roda JC | 1–0 | 1–1(aet) |
| Lille OSC | 4–3 | Dinamo Minsk | 2–1 | 2–2 |
| NK Slaven Belupo | (a)2–2 | FC Spartak Trnava | 0–0 | 2–2 |
| Tampere United | 0–1 | OFK Beograd | 0–0 | 0–1 |
| Villarreal CF | 3–2 | FC Spartak Moscow | 1–0 | 2–2 |
| FK Vėtra | 1–5 | Esbjerg fB | 1–1 | 0–4 |
Read more about this topic: 2004 UEFA Intertoto Cup
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