All draws were held at UEFA headquarters in Nyon, Switzerland.
[1] Matches may also be played on Tuesdays or Wednesdays instead of the regular Thursdays due to scheduling conflicts.
The team that scored more goals on aggregate over the two legs advanced to the next round.
In the event that aggregate score finished level, the away goals rule would be applied, i.e., the team that scored more goals away from home over the two legs advanced.
If away goals were also equal, then thirty minutes of extra time would be played, divided into two fifteen-minutes halves.
The away goals rule would again be applied after extra time, i.e., if there were goals scored during extra time and the aggregate score was still level, the visiting team would advance by virtue of more away goals scored.
If no goals were scored during extra time, the tie would be decided by penalty shootout.
[2] In the draws for each round, teams were seeded based on their 2012 UEFA club coefficients,[3] with the teams divided into seeded and unseeded pots.
The seeding in these draws (or in any cases where the results of a tie in the previous round were not known at the time of draw) was carried out under the assumption that the higher-ranked teams of the previous round would advance to this round, which means if a lower-ranked team were to advance, it would simply take the seeding of its defeated opponent.
Prior to the draws, UEFA may form "groups" in accordance with the principles set by the Club Competitions Committee, but they were purely for convenience of the draw and for ensuring that teams from the same association were not drawn against each other, and did not resemble any real groupings in the sense of the competition.
[4] The 31 winners of the play-off round qualified for the group stage to join the 7 automatic qualifiers and the 10 losing teams from the Champions League play-off round.
Aktobe Senica Borac Banja Luka Tirana Inter Baku MTK Budapest Torpedo Kutaisi Narva Trans Grevenmacher Čelik Nikšić IF Elfsborg Osijek Baku Jagodina Renova FC Santa Coloma Mura 05 Floriana Ordabasy Libertas Rosenborg Bohemians Levadia Tallinn Differdange 03
Cefn Druids Twente Sarajevo Dacia Chișinău Honvéd Rudar Pljevlja Flamurtari Celje Hibernians UE Santa Coloma Shirak Kalmar FF Gomel
Sūduva KuPS Cliftonville Llanelli Daugava Daugavpils Eschen/Mauren Víkingur Gøta Lech Poznań Metalurgi Rustavi Pyunik Olimpija Ljubljana Birkirkara Khazar Lankaran Metalurg Skopje Jeunesse Esch Zeta Zhetysu Nõmme Kalju Teuta St Patrick's Athletic Stabæk Liepājas Metalurgs Bangor City Shkëndija EB/Streymur Zimbru Chișinău
Portadown Gandzasar Kapan La Fiorita The draw for the first qualifying round was held on 25 June 2012.
2–2 on aggregate; Levadia Tallinn won on away goals.
2–2 on aggregate; St Patrick's Athletic won on away goals.
3–3 on aggregate; Čelik Nikšić won on away goals.
Lech Poznań[†] Hajduk Split Eskişehirspor
Skonto Renova[†] Khazar Lankaran[†] Young Boys Red Star Belgrade Vitesse
Vojvodina Naftan Novopolotsk Zeta[†] Zimbru Chișinău[†] Sūduva[†] Lokomotiv Plovdiv Anorthosis Famagusta Metalurh Donetsk Mladá Boleslav Aalesund Maccabi Netanya Þór[†] Levadia Tallinn[†] Čelik Nikšić[†] Tirana[†] KuPS[†] Twente[†] Servette Admira Wacker Mödling Aktobe[†] Slaven Belupo Inter Turku Portadown[†] Gandzasar Kapan[†] Milsami Orhei Žalgiris Viktoria Plzeň CSKA Sofia Rapid București Slovan Bratislava Kalmar FF[†] Metalurgi Rustavi[†] Osijek[†] Videoton Mura 05[†]
Gent Legia Warsaw Levski Sofia Anzhi Makhachkala Asteras Tripolis Sarajevo[†] Liepājas Metalurgs[†] Differdange 03[†] Honvéd[†] Inter Baku[†] Rosenborg[†] IF Elfsborg[†] Bnei Yehuda Ried Spartak Trnava Shakhtyor Soligorsk Dacia Chișinău[†] Ordabasy[†] Sligo Rovers Shirak[†]
Ruch Chorzów St Patrick's Athletic[†] Tromsø Senica[†] Široki Brijeg Olimpija Ljubljana[†] Metalurg Skopje[†] Dila Gori The draw for the second qualifying round was held on 25 June 2012, immediately after the first qualifying round draw.
Marseille Sparta Prague Lech Poznań[†] Gent[†] Sarajevo[†] Red Star Belgrade[†] Omonia Videoton[†] Eskişehirspor[†]
Admira Wacker Mödling[†] Zeta[†] Liverpool Steaua București Young Boys[†] Bursaspor Dynamo Moscow Mura 05[†] Arsenal Kyiv Kalmar FF[†] Dundee United KuPS[†] Spartak Trnava[†] Gomel[†] Athletic Bilbao Hannover 96 Rosenborg[†] Marítimo Legia Warsaw[†] Anzhi Makhachkala[†] Vitesse[†] Asteras Tripolis[†] Ried[†] Servette[†] St Patrick's Athletic[†] Slaven Belupo[†] Internazionale
Heerenveen Viktoria Plzeň[†] Rapid Wien IF Elfsborg[†] Rapid București[†] Hajduk Split[†] Horsens Aalesund[†] Ruch Chorzów[†] Vojvodina[†] Twente[†]
Anorthosis Famagusta[†] Genk Metalurh Donetsk[†] Mladá Boleslav[†] Bnei Yehuda[†] Dila Gori[†] Aktobe[†] Tromsø[†] The draw for the third qualifying rounds was held on 20 July 2012.
0–0 on aggregate; Red Star Belgrade won 6–5 on penalties.