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The 20-year-old played a key role in helping Bayern win the league and cup double last season with some impressive displays.
He also helped Germany to a third-place finish at the World Cup finals in South Africa, where he finished as the tournament's top scorer with five goals.
"Bayern rewards performance and Thomas Mueller's performances last season were extraordinary," Bayern president Karl-Heinze Rummenigge said.
"Thomas has given us a lot of joy, he won the German league title and German Cup, and played in the Champions League final....we are very happy to know that his long term future is with Bayern."