A partire da questa edizione, il club proveniente dall’Intertoto che percorrerà il cammino più lungo nella successiva edizione della Coppa Uefa verrà proclamato vincitore della Coppa Intertoto.

PRIMO TURNO

FK Pobeda Prilep (MKD)

-

Farul Constanta (ROU)

2-2

0-2

UE Sant Julià (AND)

-

NK Maribor (SVN)

0-3

0-5

Ethnikos Achnas (CYP)

-

FK Partizani Tiranë (ALB)

4-2

1-2

HSK Zrinjski Mostar (BIH)

-

Marsa FCxlokk FC (MLT)

3-0

1-1

Kilikia Yerevan (ARM)

-

Dinamo Tbilisi (GEO)

1-5

0-3

Shakhtyor Qaraghandy (KAZ)

-

MTZ-RIPA Mensk (BLR)

1-5

3-1

FK Nitra (SVK)

-

CS Grevenmacher (LUX)

6-2

6-0

MKT-Araz Imisli (AZE)

-

FC Tiraspol (MDA)

1-0

0-2

(1)

ÍBK Keflavík (ISL)

-

Dungannon Swifts FC (NIR)

4-1

0-0

Dinaburg Daugavpils (LVA)

-

HB Tórshavn (FRO)

1-1

1-0

Tampere United (FIN)

-

Carmarthen Town AFC (WAL)

5-0

3-1

Trans Narva (EST)

-

Kalmar FF (SWE)

1-6

0-2

Vetra Vilnius (LTU)

-

Shelbourne FC Dublin (IRL)

0-1

0-4

(1): dopo i tempi supplementari.

SECONDO TURNO

FC Sopron (HUN)

-

Kayserispor (TUR)

3-3

0-1

Farul Constanta (ROU)

-

Lokomotiv Plovdiv (BUL)

2-1

1-1

FK Zeta Golubovci (MNE)

-

NK Maribor (SVN)

0-3

0-2

Maccabi Petah Tikva (ISR)

-

HSK Zrinjski Mostar (BIH)

1-1

3-1

NK Osijek (CRO)

-

Ethnikos Achnas (CYP)

2-2

0-0

Grasshopper-Club (SUI)

-

FK Teplice (CZE)

2-0

2-0

FK Nitra (SVK)

-

Dnipro Dnipropetrovsk (UKR)

2-1

0-2

SV Ried (AUT)

-

Dinamo Tbilisi (GEO)

3-1

1-0

FC Tiraspol (MDA)

-

KS Lech Poznan (POL)

1-0

3-1

FK Moskva (RUS)

-

MTZ-RIPA Minsk (BLR)

2-0

1-0

Hibernian FC Edinburgh (SCO)

-

Dinaburg Daugavpils (LVA)

5-0

3-0

OB Odense (DEN)

-

Shelbourne FC Dublin (IRL)

3-0

0-1

Lillestrøm SK (NOR)

-

ÍBK Keflavík (ISL)

4-1

2-2

Tampere United (FIN)

-

Kalmar FF (SWE)

1-2

2-3

TERZO TURNO

AJ Auxerre (FRA)

-

Farul Constanta (ROU)

4-1

0-1

Larisa AE (GRE)

-

Kayserispor (TUR)

0-0

0-2

Villarreal CF (ESP)

-

NK Maribor (SVN)

1-2

1-1

Maccabi Petah-Tikva (ISR)

-

Ethnikos Achnas (CYP)

0-2

3-2

Grasshopper-Club (SUI)

-

KAA Gent (BEL)

2-1

1-1

Olympique de Marseille (FRA)

-

Dnipro Dnipropetrovsk (UKR)

0-0

2-2

BSC Hertha Berlin (GER)

-

FK Moskva (RUS)

0-0

2-0

SV Ried (AUT)

-

FC Tiraspol (MDA)

3-1

1-1

NEWCASTLE UNITED FC (ENG)

-

Lillestrøm SK (NOR)

1-1

3-0

Kalmar FF (SWE)

-

FC Twente ‘65 Enschede (NED)

1-0

1-3

OB Odense (DEN)

-

Hibernian FC Edinburgh (SCO)

1-0

1-2

Qualificati alla Coppa Uefa 2006/07: AJ Auxerre (FRA), Kayserispor (TUR), NK Maribor (SVN), Ethnikos Achnas (CYP), Grasshopper-Club (SUI), Olympique de  Marseille (FRA), BSC Hertha Berlin (GER), SV Ried (AUT), Newcastle United FC (ENG), FC Twente ‘65 Enschede (NED), OB Odense (DEN).