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Bremen's goalkeeper has been feeling Achilles tendon problems for the past few months, which resulted in him playing only 11 German league matches this season.
The operation, followed by a three-month recovery period, was supposed to be performed on Thursday.
"I will start my rehabilitation on Friday. After two weeks, I will train in the pool and start running. In the best case scenario, I will return to the team after ten weeks," said F. Baumann.
"Werder" will have to play without their captain, who has been with the team since 1999, in the UEFA Cup matches.