The first round matches of the 2006–07 UEFA Cup were played on 14 and 28 September 2006, which narrowed clubs down to 40 teams in preparation for the group stage.
^UEFA ordered Trabzonspor's home leg on 14 September to be played behind closed doors after objects were thrown at visiting fans and the fourth official, and a smoke bomb ignited in the stands, during their second qualifying round home leg against Cypriots APOEL. Trabzonspor appealed, and UEFA rejected the appeal on 13 September. Trabzonspor's penalty includes a second closed-doors game, a penalty which has been deferred for two years and will be removed if no further incidents occur.
^Due to the armed conflict in Israel, UEFA had ruled that European tournament matches could not be played in Israel until further notice. Maccabi Haifa's home leg on 14 September was moved to Nijmegen, Netherlands. On 15 September, UEFA lifted the ban, allowing future matches to be played in the Tel Aviv area.[4] Hapoel Tel Aviv were able to play their home leg in Tel Aviv on 28 September.
Note: Between the 1999–2000 and 2008–09 seasons, the competition was still known as the UEFA Cup. All seasons are included following the competition's absorption of the Cup Winners' Cup.