The 2006 UEFA Intertoto Cup was the first edition after a major change of the competition format. There were only three rounds instead of five, and eleven tournament co-winners qualified for the second qualifying round of the UEFA Cup (instead of three teams qualifying for the first round proper). 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. This honour went to Newcastle United.
*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]
*After consultations with UEFA, Italian qualifier Palermo was withdrawn by the Italian Football Federation (FIGC) on 6 June 2006. Due to the ongoing match-fixingscandal 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. They then went on to qualify for the last 16. Captain Scott Parker was presented with a certificate commemorating the triumph at St James Park before their tie with AZ.