2These clubs qualified for this season's UEFA competitions as members of the Football Association of Serbia and Montenegro during the 2005–06 season but are currently members of the Football Association of Serbia which is the official successor of the previous football association.
4Due 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. Hapoel Tel Aviv were able to play their home leg in Tel Aviv on 28 September.
5UEFA 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.
The top three teams (highlighted in green) of each group qualified for the next round. Based on paragraph 4.06 in the UEFA regulations for the current season, if two or more teams are equal on points on completion of all the group matches, the following criteria are applied to determine the rankings:
superior goal difference from all group matches played;
higher number of goals scored in all group matches played;
higher number of goals scored away in all group matches played;
higher number of wins;
higher number of away wins;
higher number of coefficient points accumulated by the club in question, as well as its association, over the previous five seasons (see paragraph 6.03 of the UEFA regulations).
2 On 19 January, UEFA declared that Feyenoord had been removed after a member of their crowd threw a glass of beer at Morten Gamst Pedersen in their home group stage match against Blackburn Rovers. UEFA announced on 25 January that Tottenham Hotspur had received a bye. This was confirmed after the final appeal.