Agger scored his second goal for the club in a Football League Cup away game against Birmingham City with a volley from close range during the seven minutes of first-half stoppage time. His third was against Arsenal, scoring a header in a 4–1 victory played on 31 March 2007. In the first semi-final of the 2006–07 Champions League, Agger received some criticism as Liverpool lost to Chelsea 1–0, after Chelsea striker Didier Drogba managed to dribble past him before making the assist to win the game. In the second leg of the semi-finals, Agger answered his critics by scoring another curler from a smartly-taken Steven Gerrard free-kick from just outside the penalty area, and helping Liverpool keep a clean sheet as the team beat Chelsea 1–0 on 1 May 2007. He went on to play in the 2007 UEFA Champions League Final which Liverpool lost 2–1 to Milan.