[7] During his first half-season at Liverpool, injuries limited Agger to four first-team appearances, and he missed the club's victory in the 2006 FA Cup Final.

[3] 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.

[14] 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.

[15] Agger started the 2007 pre-season scoring two goals in four games, including a left footed-finish against Hong Kong outfit South China.

[16] In January 2008, Agger began training and was attempting to regain match fitness, but a recurrence of the injury in his second metatarsal again ruled him out of action.

[22] Profiting in part from Škrtel's injury, Agger returned to the starting line up against Wigan for his first Premier League match of the season.

Agger was, however, at least partly to blame for Wigan taking the lead when he lost the ball to Zaki after a pass from goalkeeper Reina.

[25] Agger underwent surgery for a recurring back injury in August 2009 and made his return on 25 October 2009 for the 2–0 win over rivals Manchester United at Anfield.

[27] Agger played another 14 times in 2009–10, including scoring his seventh goal for the club, an outstanding backheel, against Benfica in the UEFA Europa League,[28] and also helped Liverpool reach the semi-finals of the same competition.

[30] Martin Škrtel was preferred rather than Agger under Roy Hodgson and he threatened to quit the club with Juventus reportedly interested in him.

On 26 February 2012, he helped Liverpool to win their first trophy since 2006 as they won the 2012 Football League Cup Final but injured his ribs during the match.

[35] On 7 April 2012, Agger made his return from injury as a second-half substitute against Aston Villa at Anfield, replacing José Enrique and hitting the crossbar with a header late on which led to the equalizer in a 1–1 draw.

[36] Agger made his first start of the league campaign in a 3–0 defeat to West Bromwich Albion on 18 August, in which he conceded a penalty and was sent off for a foul on Shane Long.

On 30 August 2014, Liverpool confirmed that Agger had rejoined his previous club Brøndby IF on a two-year deal, which involved a considerable pay cut, for a fee of £3 million.

Agger spent the next national team match on the bench before playing the full 4–1 friendly win on 17 August against England, alongside Per Nielsen.

On 7 September, he scored his first international goal in a 6–1 home win over Georgia in the nation's unsuccessful campaign to qualify for the 2006 FIFA World Cup.

Agger scored on 2 June 2007 in a 3–3 home draw against rivals Sweden for UEFA Euro 2008 qualification; the game was abandoned in the last minute for crowd misbehaviour and awarded to the Swedes.

In the finals in South Africa, Agger scored an own goal to open a 2–0 loss to the Netherlands in the first game; Simon Poulsen had headed the ball into him while trying to clear Robin van Persie's cross.

[52] Under Agger's captaincy, the Danes qualified for UEFA Euro 2012 in Poland and Ukraine, and he was again a fixture in a group stage elimination.

On 15 October 2013, Agger scored two penalties in a 6–0 home win against the Maltese in 2014 FIFA World Cup qualification, securing second place in their group.

[53] The following 28 May, from the penalty spot in added time, he scored the only goal of a win over Sweden in a match celebrating the 125th anniversary of the Danish Football Association.

Agger selected Volbeat's The Garden's Tale as his choice for the "LFC Athens 2007 Playlist" in the buildup of Liverpool's 2007 UEFA Champions League Final appearance.

He also features an intricate band around his left elbow which includes the phrase "Succes er at leve som man selv vil" ("Success is to live as you wish" in Danish).

In August 2012, during a period of intense speculation regarding his future at the club, Agger had the letters "YNWA" tattooed on the fingers of his right hand, referencing the anthem of Liverpool F.C., "You'll Never Walk Alone".

He also invested in Tattoodo together with friends, Christian Stadil, the owner of Hummel International and a famous tattooist, Ami James.

Agger invited several big names as former Liverpool stars, Pepe Reina and Steven Gerrard, to his charity events in Copenhagen.