Preliminary Round
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
Olympique Lyon  | 2–0 | 2–1 |  Ferencváros | 4–1 | – |
VPS Vaasa  | 1–2 | 0–3 |  Panathinaikos | 1–5 | – |
FC Groningena  | 1–0 | 1–2 |  ASA Tirgu Mures | 2–2 | – |
Vorskla Poltava  | 1–3 | 3–0 |  KF Laçi | 4–3 | – |
Odd Grenland  | 2–2 | 0–2 |  Trabzonspor | 2–4 | – |
Rubin Kazan  | 3–1 | 2–1 |  Wolfsberger AC | 5–2 | – |
Manchester United  | 2–0 | 4–0 |  Shakhtior Saligorsk | 6–0 | – |
Sampdoria  | 4–0 | 3–1 |  Cherno More Varna | 7–1 | – |
Hapoel Beer-Sheva  | 3–2 | 1–3 |  Sevilla | 4–5 | – |
Borussia Mönchengladbach  | 2–0 | 4–1 |  Spartaks Jurmala | 6–1 | – |
Jagiellonia Bialystok  | 1–0 | 0–2 |  CF Os Belenenses | 1–2 | – |
AIK Stockholm  | 2–1 | 0–2 |  Standard Liège | 2–3 | – |
Celtic  | 1–0 | 1–1 |  Lokomotiva Zagreb | 2–1 | – |
Omonia Nicosia  | 3–1 | 0–2 |  FC Københavna | 3–3 | – |
Dundalk  | 2–2 | 1–2 |  FK Jablonec | 3–4 | – |
FC Zürich  | 2–2 | 2–1 |  Vikingur Reykjavik | 4–3 | – |
First Round
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
| Hajduk Split | 1–2 | 0–0 | Arsenal | 1–2 | – |
| Dinamo Minsk | 2–2 | 2–4 | Ajax | 4–6 | – |
| Steaua Bucuresti | 0–1 | 2–3 | Galatasaray | 2–4 | – |
| Villarreal | 1–2 | 5–1 | FK Kukësi | 6–3 | – |
| Slovan Liberec | 2–1 | 3–2 | FC Salzburg | 5–3 | – |
| Brøndby IF | 0–3 | 1–3 | Napoli | 1–6 | – |
| Lokomotiv Moscow | 2–0 | 3–0 | FC Zürich | 5–0 | – |
| Club Brugge | 2–0 | 3–2 | FC Lahti | 5–2 | – |
| Olympique Marseille | 1–0 | 1–1 | Vorskla Poltava | 2–1 | – |
| Manchester United | 7–0 | 2–1 | FC Thun | 9–1 | – |
| Schalke 04 | 3–1 | 2–2 | Aberdeen | 5–3 | – |
| Rubin Kazan | 3–1 | 2–0 | FC Botosani | 5–1 | – |
| Bayer Leverkusen | 2–1 | 2–2 | Apollon Limassol | 4–3 | – |
| PAOK Thessaloniki | 2–2 | 3–0 | IF Elfsborg | 5–2 | – |
| Viktoria Plzen | 2–0 | 0–1 | Lech Poznan | 2–1 | – |
| Beitar Jerusalem | 1–2 | 0–3 | FC Porto | 1–5 | – |
| Uni College Dublin | 0–3 | 0–2 | Sporting CP Lisbon | 0–5 | – |
| Litex Lovech | 0–0 | 0–2 | Trabzonspor | 0–2 | – |
| Olympique Lyon | 2–0 | 2–2 | Asteras Tripolis | 4–2 | – |
| CF Os Belenenses | 2–0 | 3–0 | FK Jablonec | 5–0 | – |
| FC Groningen | 3–2 | 0–3 | CSKA Moscow | 3–5 | – |
| FC København | 1–1 | 0–2 | Liverpool | 1–3 | – |
| AS Monaco | 1–1 | 2–3 | KR Reykjavik | 3–4 | – |
| Dnipro Dnipropetrovsk | 1–2 | 1–1 | Celtic | 2–3 | – |
| Besiktas | 2–0 | 0–3 | Panathinaikos | 2–3 | *– |
| SCR Altach | 1–2 | 2–4 | AZ Alkmaar | 3–6 | – |
| Sampdoria | 2–0 | 1–1 | Rosenborg BK | 3–1 | – |
| Videoton Fehérvár | 2–2 | 0–5 | Fiorentina | 2–7 | – |
| FK Jelgava | 2–4 | 0–5 | Anderlecht | 2–9 | – |
| Zorya Luhansk | 0–1 | 3–1 | Sevilla | 3–2 | – |
| Borussia Mšnchengladbach | 3–3 | 2–1 | Standard Liège | 5–4 | – |
| FC Sion | 1–3 | 0–0 | Real Sociedad | 1–3 | – |
Second Round
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
| AZ Alkmaar | 0–0 | 0–3 | Napoli | 0–3 | – |
| Manchester United | 2–2 | 2–1 | Celtic | 4–3 | – |
| Galatasaray | 3–0 | 2–1 | PAOK Thessaloniki | 5–1 | – |
| Club Brugge | 2–0 | 0–0 | Rubin Kazan | 2–0 | – |
| KR Reykjavik | 1–2 | 0–4 | Ajax | 1–6 | – |
| Olympique Lyon | 1–3 | 0–1 | Viktoria Plzen | 1–4 | – |
| Fiorentinaa | 2–1 | 0–1 | Sampdoria | 2–2 | – |
| Lokomotiv Moscow | 0–1 | 2–0 | Anderlecht | 2–1 | – |
| Slovan Liberec | 0–1 | 0–2 | Real Sociedad | 0–3 | – |
| Villarreal | 2–1 | 2–2 | Panathinaikos | 4–3 | – |
| Zorya Luhansk | 3–2 | 3–0 | Liverpool | 6–2 | – |
| Schalke 04 | 2–0 | 1–2* | CSKA Moscow | 3–2 | – |
| Bayer Leverkusen | 3–2 | 3–3 | Sporting CP Lisbon | 6–5 | – |
| Trabzonspor | 1–1 | 0–3 | Borussia Mönchengladbach | 1–4 | – |
| CF Os Belenenses | 2–0 | 0–1 | FC Porto | 2–1 | – |
| Arsenal | 0–2 | 0–3 | Olympique Marseille | 0–5 | – |
Third Round
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
| Bayer Leverkusen | 2–2 | 1–2 | Galatasaray | 3–4 | – |
| Viktoria Plzena | 2–1 | 2–3 | Ajax | 4–4 | – |
| Borussia Mönchengladbach | 2–2 | 0–2 | Lokomotiv Moscow | 2–4 | – |
| Villarreal | 2–0 | 2–1 | Sampdoria | 4–1 | – |
| Real Sociedad | 2–0 | 1–1 | Olympique Marseille | 3–1 | – |
| Napoli | 4–1 | 0–0 | Club Brugge | 4–1 | – |
| CF Os Belenenses | 3–1 | 1–4* | Manchester United | 4–5 | – |
| Schalke 04a | 1–1 | 2–2 | Zorya Luhansk | 3–3 | – |
Quarter-Final
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
| Viktoria Plzena | 0–1 | 3–2 | Manchester United | 3–3 | – |
| Villarreal | 0–1 | 1–2 | Galatasaray | 1–3 | – |
| Schalke 04 | 2–1 | 0–1 | Lokomotiv Moscow | 2–2 | – |
| Real Sociedada | 3–0 | 1–4 | Napoli | 4–4 | – |
Semi-Final
| Team 1 | 1st leg | 2nd leg | Team 2 | Agg | Pens |
|---|
| Lokomotiv Moscow | 2–1 | 0–3 | Real Sociedad | 2–4 | – |
| Galatasaray | 2–1 | 3–2 | Viktoria Plzen | 5–3 | – |
Final
| Team 1 | 1st leg | Team 2 | Pens |
|---|
| Real Sociedad | 3–0 | Galatasaray | – |
|
