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Croatia is charged with "improper conduct" of supporters, including "racist chants, racist symbols" at a game in Poznan on Thursday, UEFA said in a statement.
UEFA received reports from anti-discrimination monitors working with Football Against Racism in Europe, who wrote that Croatia fans made monkey noises and displayed far-right nationalist flags.
Balotelli, who is black, started the game for Italy against Croatia, and was replaced in the second half of the 1-1 draw.
"It was fairly consistent throughout the game," FARE executive director Piara Powar told The Associated Press. "It was at its most intense as he was substituted and left the field."
The charge also relates to fireworks thrown on the field after Croatia scored, which delayed Italy's kickoff to restart the game.
UEFA said its disciplinary panel will judge the case against Croatia on Tuesday.
The Croatia association, known by its initials HNS, said it condemned the incident and "distances itself from all deviant behavior on the part of the fans."
Those responsible were "not supporters, but hooligans who should be isolated from all sports events," the Croatian body said in a statement, appealing to UEFA "not to punish the Croatian national team."
UEFA rules make national associations responsible for their fans' behavior. Punishments range from warnings and a sliding scale of fines to points deductions and even expulsion from Euro 2012.
Four years ago, UEFA fined Croatia 20,000 Swiss francs (then $19,600; ?12,450) for its fans' neo-Nazi flags and chants during a Euro 2008 quarterfinals loss against Turkey in Vienna, Austria.
Also in 2008, FIFA fined Croatia fined 30,000 Swiss francs (then $27,700; ?18,800) after England forward Emile Heskey was subjected to racist abuse during a World Cup qualifying match in Zagreb.
UEFA is also studying reports that a banana was thrown toward the field from a section housing Croatia fans in Poznan.
Balotelli has now been the target of reported abuse at both Italy matches at Euro 2012.
UEFA is investigating claims by a Spanish fans' group that some Spain followers made monkey chants at him during a Group C match last Sunday in Gdansk.
In a separate investigation, UEFA is seeking evidence to support claims that Russian fans made monkey noises at Czech Republic defender Theodor Gebre Selassie in Wroclaw.
UEFA pledged zero tolerance of racism in Poland and Ukraine during the three-week tournament.
