2009–10 UEFA Europa League Second qualifying round Second qualifying round

| Team_1 | Agg_ | Team_2 | _1st_leg | _2nd_leg |
|---|---|---|---|---|
| Rosenborg | 0–1 | Karabakh | 0–0 | 0–1 |
| Zimbru Chişinău | 0–1 † | Paços de Ferreira | 0–0 | 0–1 |
| Juvenes/Dogana | 0–5 † | Polonia Warsaw | 0–1 | 0–4 |
| Sturm Graz | 3–2 | Široki Brijeg | 2–1 | 1–1 |
| Basel | 7–1 | FC Santa Coloma | 3–0 | 4–1 |
| Honka | 3–0 | Bangor City | 2–0 | 1–0 |
| MŠK Žilina | 3–0 | Dacia Chişinău | 2–0 | 1–0 |
| Anorthosis | 3–4 | Petrovac | 2–1 | 1–3 ( aet ) |
| St Patrick`s Athletic | 2–1 | Valletta | 1–1 | 1–0 |
| Omonia | 8–1 | HB | 4–0 | 4–1 |
| Gorica | 1–2 | Lahti | 1–0 | 0–2 |
| Sigma Olomouc | 3–1 | Fram | 1–1 | 2–0 |
| Legia Warsaw | 4–0 | Olimpi Rustavi | 3–0 | 1–0 |
| Falkirk | 1–2 | Vaduz | 1–0 | 0–2 ( aet ) |
| Elfsborg | 3–0 | Haladás | 3–0 | 0–0 |