After four season as Basel's chairman Werner Edelmann stood down and Mrs Gisela Oeri was voted as the club's very first chairwoman at the AGM.
Franco Costanzo was voted to player of season[1] Following the last minute loss of the 2005–06 Super League Championship as a result of the 1–2 home defeat against FC Zürich on 13 May 2006 and the subsequent riots, the so-called Basel Hooligan Incident, the club had to carry consequences.
[2] As well as the big fine, the first two home games of the 2006–07 Super League season were held completely without fans, as so called "ghost matches".
They started a catch up race after the winter break and finished the league campaign as runners-up, just one point behind champions FC Zürich.
Cristiano dos Santos Rodrigues played his team debut on 26 August 2006 in the Cup match against local club FC Liestal.
The match was noted as being very rough, referee René Rogalla showed the yellow card to five Lugano players.
[7] However, in the third-round game on 12 November away against second tier FC Baulmes extra time was needed before the tie was decided.
Basel played a bad first half, Bruno Berner had to clear a ball off the line, with goalkeeper Franco Costanzo already beaten.
During the extra time the hosts were visibly tired and Mile Sterjovski was able to score the winning goal for the visitors.
Aarau complained for a penalty as Demetrio Greco was brought down five minutes from the end, but referee Sascha Kever did not blow his whistle.
Luzern's keeper David Zibung became the tragic hero in the sold-out Stade de Suisse in Bern, who, according to the interpretation of referee Nicole Petignat, in the 90th minute pulled Scott Chipperfield off his feet.
"[10] Basel had missed the championship just four days earlier, but they achieved their aim of winning the cup on this Whit Monday.
In the second qualifying round they drawn against FC Vaduz from Liechtenstein, narrowly progressing on the away goals rule after a 2–2 aggregate draw.
Basel dominated the match and it was not a surprise as Eduardo struck on the hour, tapping in after Timmer could only parry Petrić's shot.
Australian defender Lucas Neill had the first goal chance for the home team after four minutes, but goalkeeper Franco Costanzo held.
15 minutes from time Tugay Kerimoğlu scored in the top left corner with a good 25 meter Sunday shot.
The disastrous referee Oleh Oriekhov gave a penalty against Basel after a clear dive and Francis Jeffers scored from the spot in the 90th minute.
It exploded into life just after the half-hour when Monsef Zerka broke down the right for the French team and cut into the area before laying off a perfectly weighted pass for Kim, who finished off nicely.
The Basel response was immediate, Reto Zanni supplying Scott Chipperfield as the Australian international broke from midfield to fire past Olivier Sorin from inside the area.
Parity was restored, however, on 56 minutes as Mile Sterjovski got the final touch to a free-kick from the influential Mladen Petrić.
Goalkeeper Franco Costanzo was only able to stop the Nancy attack by fouling Issiar Dia, which resulted in his sending off and a penalty against Basel.
Paweł Brożek then had another three or four good chances before the half time whistle from Hungarian referee Viktor Kassai.
Crayton rescues sensationally, but remained somewhat dazed lying on the pitch, because Brozek did not jump up properly and accidentally hit him on the head with his boot.
Paweł Brożek became man of the match just three minutes later as he took the pass from Jakub Błaszczykowski and netted the team's third goal, for Wisla to win, with the end result 3–1.
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