The striker may miss over a month of club football as he could be called up for international duty as early as January 5 with players required 14 days prior to the tournament, which commences on January 19.
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"The Africa Cup of Nations starts on January 19, and usually the players have to be there 14 days before - that means we could lose Gervinho on January 5," Wenger told the club's official website.
"Usually it's always a battle to get him to play in the FA Cup third round. When they come back, the players have played a massive competition.
"Last year, we never [got] him back completely because he came back with a disappointing result and we didn't give him any rest.
"Maybe we have to do it a little bit differently when he comes back [in 2013]."
Ivory Coast begin their Africa Cup of Nations campaign against Togo on January 22. They face Tunisia four days later and complete their group fixtures against Algeria on January 30.