The German centre-back could face a three-game suspension following a clash with Philippe Senderos during the club's match against Fulham in the Premier League on Saturday
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However, the FA has acted retrospectively and given Huth until 18:00GMT on Tuesday to respond to the charge.
If he is handed a suspension, he is likely to miss his side's next three matches - Premier League games against West Ham, Newcastle and West Brom.
The 28-year-old has been a regular once again under Tony Pulis this season - making 27 appearances and scoring once in the league so far.
Stoke midfielder Steven N'Zonzi clashed with Dimitar Berbatov and Bryan Ruiz in separate incidents during the game, though neither will require further action.