First Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Beitar Jerusalem FC | 6–4 | FK Sileks Kratovo | 4–3 | 2–1 |
| Bohemian F.C. | 2–3 | K.A.A. Gent | 1–0 | 1–3 |
| Tiligul Tiraspol | 2–9 | Pogoń Szczecin | 0–3 | 2–6 |
| Valletta F.C. | 2–7 | FK Budućnost Podgorica | 0–5 | 2–2 |
| Narva Trans | 1–2 | K.S.C. Lokeren Oost-Vlaanderen | 0–2 | 1–0 |
| FC Victoria Rosport | 2–5 | IFK Göteborg | 1–2 | 1–3 |
| KS Dinamo Tirana | 3–5 | NK Varteks | 2–1 | 1–4 |
| NK Slaven Belupo | 2–0 | NK Drava Ptuj | 1–0 | 1–0 |
| Lernagorts-Ararat | 1–9 | Neuchâtel Xamax | 1–3 | 0–6 |
| CFR Ecomax Cluj | 7–3 | FK Vėtra | 3–2 | 4–1 |
| Olympiakos Nicosia | 0–16 | Gloria Bistriţa | 0–5 | 0–11 |
| Skála ÍF | 0–3 | Tampere United | 0–2 | 0–1 |
| Vasas SC | 0–2 | FK ZTS Dubnica | 0–0 | 0–2 |
| FK Žalgiris Vilnius | 2–0 | Lisburn Distillery F.C. | 1–0 | 1–0 |
| FK Karvan | 1–4 | Lech Poznań | 1–2 | 0–2 |
| FC Rànger's | 1–6 | SK Sturm Graz | 1–1 | 0–5 |
| Bangor City F.C. | 1–4 | Dinaburg FC | 1–2 | 0–2 |
| FK Smederevo | 1–3 | FK Pobeda | 0–1 | 1–2 |
| FC Neman Grodno | 0–1 | FC Tescoma Zlín | 0–1 | 0–0 |
| Lombard-Pápa TFC | 3–1 | FC WIT Georgia | 2–1 | 1–0 |
| FC Inter | 4–0 | ÍA Akranes | 0–0 | 4–0 |
Read more about this topic: 2005 UEFA Intertoto Cup
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“All round and round does the world lie as in a sharp-shooter’s ambush, to pick off the beautiful illusions of youth, by the pitiless cracking rifles of the realities of age.”
—Herman Melville (1819–1891)