Group 1: Seeded
Sevilla FC (ESP) / AEK Athens FC (GRE)
AFC Rapid Bucuresti (ROU)
FC Lokomotiv Moskva (RUS)
Bolton Wanderers FC (ENG)
ACF Fiorentina (ITA)
Unseeded
FC Groningen (NED)
1. FC Nürnberg (GER)
FC Midtjylland (DEN)
FC Salzburg (AUT)
FK Rabotnicki (MKD)
Group 2: Seeded
Villarreal CF (ESP)
Bayer 04 Leverkusen (GER)
FC Zenit St. Petersburg (RUS)
Galatasaray SK (TUR)
Everton FC (ENG)
Unseeded
UD Leiria (POR)
R. Standard de Liège (BEL)
FC Metalist Kharkiv (UKR)
FC Sion (SUI)
FC BATE Borisov (BLR)
Group 3: Seeded
Panathinaikos FC (GRE)
FC Girondins de Bordeaux (FRA)
AC Sparta Praha (CZE)
Club Atlético de Madrid (ESP)
Empoli FC (ITA)
Unseeded
Odense BK (DEN)
FC Artmedia Petržalka (SVK)
FC Zürich (SUI)
Kayseri Erciyesspor (TUR)
Tampere United (FIN)
Group 4: Seeded
AZ Alkmaar (NED)
RSC Anderlecht (BEL)
FC Sochaux-Montbéliard (FRA)
UC Sampdoria (ITA)
FC Spartak Moskva (RUS)
Unseeded
Panionios GSS (GRE)
FC Paços de Ferreira (POR)
SK Rapid Wien (AUT)
Aalborg BK (DEN)
BK Häcken (SWE)
Group 5: Seeded
AFC Ajax (NED)
US Città di Palermo (ITA)
Blackburn Rovers FC (ENG)
SC Braga (POR)
Stade Rennais FC (FRA)
Unseeded
NK Dinamo Zagreb (CRO)
FK Mladá Boleslav (CZE)
PFC Lokomotiv Sofia (BUL)
Larissa FC (GRE)
Hammarby (SWE)
Group 6: Seeded
FC Bayern München (GER)
Club Brugge KV (BEL)
SC Heerenveen (NED)
FC Dnipro Dnipropetrovsk (UKR)
PFC CSKA Sofia (BUL)
Unseeded
Toulouse FC (FRA)
CF Os Belenenses (POR)
Aberdeen FC (SCO)
SK Brann (NOR)
Helsingborgs IF (SWE)
Group 7: Seeded
FC Basel 1893 (SUI)
Real Zaragoza (ESP)
Hamburger SV (GER)
FK Austria Wien (AUT)
Hapoel Tel-Aviv FC (ISR)
Unseeded
PFC Litex Lovech (BUL)
Aris Thessaloniki FC (GRE)
Vålerenga IF (NOR)
AIK Solna (SWE)
FK Sarajevo (BIH)
Group 8: Seeded
RC Lens (FRA)
Tottenham Hotspur FC (ENG)
FC Dinamo 1948 Bucuresti (ROU)
Getafe CF (ESP)
FK Crvena Zvezda (SRB)
Unseeded
FC København (DEN)
FC Twente (NED)
Groclin Grodzisk Wielkopolski (POL)
Anorthosis Famagusta FC (CYP)
IF Elfsborg (SWE)