Qualifying Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| AIK | 1–0 | Fylkir | 1–0 | 0–0 |
| Vllaznia Shkodër | 0–6 | Dundee | 0–2 | 0–4 |
| Levadia | 3–6 | Varteks | 1–3 | 2–3 |
| Esbjerg | 9–1 | FC Santa Coloma | 5–0 | 4–1 |
| Željezničar Sarajevo | 4–1 | Anorthosis | 1–0 | 3–1 |
| Hapoel Tel Aviv | 3–2 | Banants | 1–1 | 2–1 |
| Brøndby | 5–0 | Dinamo Minsk | 3–0 | 2–0 |
| Malmö | 6–0 | Portadown | 4–0 | 2–0 |
| Dinamo București | 6–3 | Liepājas Metalurgs | 5–2 | 1–1 |
| Valletta | 0–4 | Neuchâtel Xamax | 0–2 | 0–2 |
| Kärnten | 3–2 | Grindavík | 2–1 | 1–1 |
| Viktoria Žižkov | 6–1 | Zhenis | 3–0 | 3–1 |
| FK Sarajevo | 1–4 | Sartid | 1–1 | 0–3 |
| APOEL | 5–1 | Derry City | 2–1 | 3–0 |
| Litex Lovech | 0–2 | Zimbru Chişinău | 0–0 | 0–2 |
| Neman Grodno | 1–1(a) | Steaua București | 1–1 | 0–0 |
| Eztella Ettelbruck | 1–9 | Kamen Ingrad | 1–2 | 0–7 |
| Manchester City | 7–0 | Total Network Solutions | 5–0 | 2–0 |
| Molde | 6–0 | KÍ Klaksvík | 2–0 | 4–0 |
| Odense | 4–1 | TVMK | 1–1 | 3–0 |
| Ventspils | (a)3–3 | Wisła Płock | 1–1 | 2–2 |
| MyPa | 5–4 | Young Boys | 3–2 | 2–2 |
| Vaduz | 0–2 | Dnipro Dnipropetrovsk | 0–1 | 0–1 |
| Coleraine | 2–6 | União de Leiria | 2–1 | 0–5 |
| Dyskobolia Grodzisk | 6–1 | Atlantas | 2–0 | 4–1 |
| Dinamo Tirana | 1–7 | Lokeren | 0–4 | 1–3 |
| Cwmbran Town | 0–6 | Maccabi Haifa | 0–3 | 0–3 |
| Publikum | 12–2 | Belasica | 7–2 | 5–0 |
| Cementarnica 55 Skopje | (a)1–1 | GKS Katowice | 0–0 | 1–1 |
| Matador Púchov | 6–0 | Sioni Bolnisi | 3–0 | 3–0 |
| Red Star Belgrade | 8–2 | Nistru Otaci | 5–0 | 3–2 |
| Ekranas | 2–3 | Debreceni VSC | 1–1 | 1–2(aet) |
| Birkirkara | 0–6 | Ferencváros TC | 0–5 | 0–1 |
| Haka | 2–2(a) | Hajduk Split | 2–1 | 0–1 |
| Torpedo Moscow | 9–0 | Domagnano | 5–0 | 4–0 |
| Atyrau | 1–6 | Levski Sofia | 1–4 | 0–2 |
| Olimpija Ljubljana | 4–2 | Shelbourne | 1–0 | 3–2 |
| Lens | 5–0 | Torpedo Kutaisi | 3–0 | 2–0 |
| Nordsjælland | 6–0 | Shirak | 4–0 | 2–0 |
| Artmedia Petržalka | 2–0 | F91 Dudelange | 1–0 | 1–0 |
| NSÍ Runavík | 1–9 | Lyn Oslo | 1–3 | 0–6 |
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