The 2006 UEFA Intertoto Cup was the first edition after a major change of the competition format.

Also, for the first time in the modern history of the competition, an outright winner was highlighted from the 11 co-winners of the Cup, with that honour going to the final-round Intertoto winner that advanced farthest in the UEFA Cup.

* FK Zeta qualified for this season's UEFA competitions as member of the Football Association of Serbia and Montenegro during the 2005/06 season but was at the time of that match already a member of the Football Association of Montenegro.

[3] 1The match was played at FK Partizan's ground in Belgrade, Serbia, because FK Zeta's ground in Golubovci doesn't meet UEFA standards 2The match was played in Herzliya because Maccabi Petah Tikva's ground in Petah Tikva is undergoing renovations Kayserispor won 4–3 on aggregate.

Maccabi Petah Tikva won 4–2 on aggregate.

2–2 on aggregate, Ethnikos Achna won on away goals rule.

Due to the ongoing match-fixing scandal in Italy, the FIGC could not officially confirm the 2005–06 Serie A standings in time for Palermo to compete in the Intertoto Cup and therefore French club Auxerre replaced Palermo, according to UEFA regulations governing the Intertoto Cup.

Eight of the eleven co-winners which entered the UEFA Cup via the Intertoto Cup won their qualifying ties and progressed to the first round proper.

Half of these eight survived the first round and entered the group stages, only Newcastle United secured a place in the UEFA Cup Round of 32 and were the last remaining team from the Intertoto Cup – making them the outright winner.

Captain Scott Parker was presented with a certificate commemorating the triumph at St James Park before their tie with AZ.