Rudiger, who started in both of Germany's World Cup qualifier matches this month, was not named in Real's squad list for Saturday's LaLiga match at Real Sociedad, Spanish media reports said.
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"Following tests conducted on Toni Rüdiger by the Real Madrid Medical Services, he has been diagnosed with an injury to the rectus femoris muscle in his left leg," Real said in a statement.
Real did not say how long Ruediger will be out for.
Rudiger, 32, underwent knee surgery in April for a partial tear in the external meniscus. The former Roma and Chelsea player returned to action in June at the Club World Cup.