The club did not specify the length of the new deal, but it is thought to be a two-year extension to his current agreement, tying him to Anfield until 2016.
Agger said: "It means everything to me. This is where I want to be and I'm happy the club want me. I am really happy right now. I've never wanted to go anywhere else.
"I feel I am a part of this club - and I want to be a part of this club in the future.
"I like the way it is going right now with the style we're playing, and hopefully the results will come soon as well."
The Dane joined Liverpool in January 2006, though his time at the club has been disrupted by injuries.