Hernandez, part of the French team who won the 2018 World Cup, will join Bayern on 1 July on a five-year contract.
The Bundesliga outfit said it had been discovered during the 23-year-old’s medical that he had suffered damage to the medial collateral ligament in his right knee, and that following discussions with Atletico, he was to undergo surgery on Wednesday.
Hernandez said on Bayern’s official website: “This is a really important day in my footballing career. FC Bayern Munich is one of the best clubs in Europe and the world. I’m proud to be able to fight for all possible titles with Bayern.”
Bayern said Hernandez, who came through Atletico’s youth set-up after joining them in 2007, was expected to be available for the start of next season.
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