Star striker Eren Derdiyok was sold to Bayer 04 Leverkusen and Eduardo Rubio returned to Cruz Azul because his loan was not made permanent.

However, after Alberto Regazzoni was cautioned for a foul on Valentin Stocker in the 23rd minute, Basel won control of the game and home goalkeeper Marco Wölfli was forced to make a good save following Scott Chipperfield's left footed shot.

Then, exactly on the hour, a left footed cross from Stocker found Scott Chipperfield unmarked in front of goal and he was able to head home and give Basel a 2–0 win.

Basel were drawn against FC Le Mont-sur-Lausanne, who at that time were semi-professional and played in the Challenge League, the second tier of Swiss football.

In the second minute of over-time Alexandre Alphonse was lucky to collect a diagonal ball from his teammate and he netted to make the final score 4–2 for the home team, who thus advanced to the quarterfinals.

Although immediately after the restart Dennis Hediger pulled a goal back for the visitors the game was decided and Basel won 3–1 to advance to the semi-finals.

Basel were missing goalkeeper Franco Costanzo, midfielder Cabral, and their two Swiss international forwards Alexander Frei and Marco Streller due to injury.

Basel's midfielder Marcos Gelabert played a long diagonal cross from the left side, defender Patrik Baumann was unable to clear the ball and Federico Almerares, who was positioned behind him, put the favorites a goal up.

The captain of the Swiss international team Alexander Frei came on as a substitute in the 67th minute, making his comeback after being out injured fracture of his right arm since February.

Basel were clear favorites to win the match and so new head-coach Thorsten Fink used the opportunity to bring some young players from the U-21 team into the squad.

Five minutes before the break Santa Coloma's Argentinian defender José Daniel Álvarez was unlucky and deflected a ball passed his own goalkeeper.

Three minutes from time substitute Federico Almerares ran clear and scored his goal to and the match ended with a 4–1 away victory for Basel, thus victors with a 7–1 on aggregate.

Basel had started well, but the goal scored by Alexander Frei after four minutes was disallowed due to an off-side decision by Spanish referee Fernando Teixeira Vitienes.

Head-coach Thorsten Fink again made multipal changes to the starting eleven, but the players understood themselves well and played an attacking football with both Alexander Frei and Marco Streller coming to early chances.

The game calmed from then immediately and both teams played well, especially the visitors, but it was Fernando Nestor Pérez who put the locals 1–0 ahead just after half time.

Basel head-coach Thorsten Fink then reacted and substituted in the two attacking midfielders Carlitos and Xherdan Shaqiri for the defensive players Samuel Inkoom and Behrang Safari.

The players were still celebrating their first success and did not concentrate as Baku played a fast counter-attack, Felipe Almeida Félix took his chance and put the teams level again.

A loose ball fell in front of Cabral's feet and he immediately passed it to Carlitos, who, with a first-time drive from about 30 metres found the bottom corner of the goal.

Francesco Totti sent a dipping free-kick which hit the top of the crossbar and John Arne Riise's long-range drive was deflected wide.

A late breakaway by substitute Federico Almerares earned Basel an impressive victory and the three points, just three minutes from time, as he was sent clear by Frei and calmly rounded Júlio Sérgio to score and make it a 2–0 win.

[20] Matchday 2 in the group stage saw Basel make their first ever visit to Craven Cottage and some 16,000 supporters were in the stadium to see a tight encounter between Fulham and the visitors.

Basel started well and were in charge of the game, as in the 13th minute as their winger Behrang Safari out ran Fulham defender Stephen Kelly wide on the touchline and he played an exact pass to Alexander Frei, but the striker placed his shot the wrong side of the post.

Basel still played somewhat better, but Fulham captain Danny Murphy struck with a low drive in the 57th minute and this remained the only goal of the game, as his side then won 1–0 to climb to the top of Group table.

Basel took the lead in the 20th-minute, as Marco Streller let a long ball bounce past him to Alexander Frei, who was able to chest it down and place his shot beyond keeper Ivan Karadzhov who was rushing towards him.

Basel head coach Thorsten Fink was forced to change his team because of injuries to goalkeeper Franco Costanzo, defender David Abraham and midfielders Carlitos and Antônio da Silva.

After 35 minutes Marcos Gelabert opened the score, as Valentin Stocker laid the ball into his path and his 20-metre shot was slightly deflected as it made its way into the goal, beyond the reach of keeper Zdravko Chavdarov.

In the 61st minute CSKA came back into the match as Marquinhos's corner flew over all the central players and found Todor Yanchev, who was able to control the ball with his chest and to score with a looping shot beyond goalkeeper Massimo Colomba.

Then Cicinho's cross flew high into the penalty area, Marcos Gelabert pulled back Francesco Totti and referee Tony Chapron from the French Football Federation whistled for a spot-kick.

Roma then increased their pressure again and a series of first-time passes ended with Daniele De Rossi playing the ball behind the Basel back line to Mirko Vučinić and his left-footed shot put his team into the lead.

During the closing stages Marco Streller forced keeper Sérgio to make a save with his feet and Alexander Frei hit the cross-bar but the visitors were unable to equalise.