| 1st leg | 2nd leg | Agg. | |
| Shakhter Karagandy vs Klaipedos Atlantas | 0-0 | 3-0 | 3-0 |
| Hapoel Beer Sheva vs RNK Split | 1-2 | 0-0 | 1-2 |
| Myllykosken Pallo-47 vs Dinamo Minsk | 0-3 | 0-0 | 0-3 |
| Omonia Nicosia vs Buducnost Podgorica | 2-0 | 0-0 | 2-0 |
| FC Krasnodar vs JK Sillamae Kalev | 4-0 | 5-0 | 9-0 |
| FK Haugesund vs FK Sarajevo | 1-0 | 1-3 | 2-3 |
| Inter Baku vs IF Elfsborg* | 1-0 | 0-1 | 1-1 |
| AIK Solna vs Linfield | 0-1 | 2-0 | 2-1 |
| Chikhura* vs Bursaspor Sachkhere | 0-0 | 0-0 | 0-0 |
| Esbjerg fB vs Kairat Almaty | 1-1 | 1-0 | 2-1 |
| FC Vaduz vs Ruch Chorzow | 2-3 | 0-0 | 2-3 |
| Flamurtari vs Petrolul Ploiesti | 0-2 | 1-3 | 1-5 |
| Hapoel Tel Aviv vs FC Astana | 0-3 | 1-0 | 1-3 |
| IFK Gothenburg vs Gyori ETO | 3-0 | 0-1 | 3-1 |
| Lech Poznan vs JK Nomme Kalju | 0-1 | 3-0 | 3-1 |
| Slovan Liberec vs MFK Kosice | 1-0 | 3-0 | 4-0 |
| SV Groedig vs FK Cukaricki | 4-0 | 1-2 | 5-2 |
| Shakhtyor Soligorsk vs Derry City | 1-0 | 5-1 | 6-1 |
| Tromso vs Vikingur | 0-0 | 1-2 | 1-2 |
| FC Zimbru Chisinau** vs CSKA Sofia | 1-1 | 0-0 | 1-1 |
| FC Groningen vs Aberdeen | 0-0 | 1-2 | 1-2 |
| Spartak Trnava vs Zestafoni | 0-0 | 3-0 | 3-0 |
| Zorya Luhansk vs KF Laci | 3-0 | 2-1 | 5-1 |
| Asteras Tripolis vs RoPS Rovaniemi | 1-1 | 4-2 | 5-3 |
| Sligo Rovers vs Rosenborg | 2-1 | 1-3 | 3-4 |
| Vojvodina vs AS Trencin | 0-4 | 3-0 | 3-4 |
| Zawisza Bydgoszcz vs Zulte Waregem | 1-2 | 1-3 | 2-5 |
| Hajduk Split vs Dundalk | 2-0 | 1-2 | 3-2 |
| Diosgyor VTK vs Litex Lovech | 2-0 | 1-2 | 3-2 |
| Ferencvaros vs Rijeka | 0-1 | 1-2 | 1-3 |
| Gorica vs Molde | 1-4 | 1-1 | 2-5 |
| FK Jagodina vs CFR Cluj | 0-0 | 0-1 | 0-1 |
| Koper vs FK Neftchi | 2-1 | 0-2 | 2-3 |
| Siroki Brijeg vs Mlada Boleslav | 1-2 | 0-4 | 1-6 |
| Crusaders vs Brommapojkarna | 0-4 | 1-1 | 1-5 |
| St Johnstone* vs FC Lucerne | 1-1 | 1-1 | 2-2 |
| St Polten vs Botev Plovdiv | 1-2 | 2-0 | 3-2 |
| FH Hafnarfjordur vs Neman Grodno | 1-1 | 2-0 | 3-1 |
| Stjarnan vs Motherwell | 2-2 | 3-2aet | 5-4 |
| Zeljeznicar vs Metalurg Skopje** | 0-0 | 2-2 | 2-2 |
* Through on penalties. ** Through on away goals.