The German centre-back responded to tweets sent from an account which posts sexual images and invites users to guess the gender of individuals in the pictures.
Huth deleted the tweets and later issued an apology for any offence caused by his actions.
He tweeted: "Clearly no offence was meant or directed to anyone, but apologies if I've offended anyone."
However, Huth could now face a suspension after the FA revealed on Wednesday that the former Chelsea man has been charged for his use of social media.
A statement on the governing body's official website said: "Stoke City's Robert Huth has been charged for misconduct in relation to comments posted on social media.
"It is alleged the comments were indecent and/or improper and/or brought the game into disrepute, contrary to FA Rule E3(1).
"It is further alleged that this breach of Rule E3(1) is an “Aggravated Breach” as defined in Rule E3(2), as it included a reference to gender and/or gender reassignment.
"Huth has until 6pm on 21 January 2015 to respond to the charge."
Huth has been linked with a loan move this month after falling down the pecking order at Stoke under Mark Hughes.
