It was investigating reports a banana was thrown on to the pitch during the Group C match with Italy on Thursday.
A photographer reportedly saw a steward retrieving a banana and heard monkey chants directed at Mario Balotelli.
The disciplinary proceedings are outlined for “racist chants, racist symbols” in the crowd.
“UEFA has opened disciplinary proceedings against the Croatian Football Federation for the setting-off and throwing of fireworks, and the improper conduct of supporters (racist chants, racist symbols) at the UEFA Euro 2012 Group C match against Italy in Poznan on Thursday,” it said in a statement.
The UEFA Control and Disciplinary Body will deal with the case on Tuesday, 19 June.
FARE (Football Against Racism in Europe) announced on Friday that their observers heard between 300 and 500 Croatia fans chanting monkey noises, which prompted Uefa to investigate the matter.
The Croatian Football Federation (HNS) has condemned the “deviant” fans who had shamed their country but urged UEFA to spare them further sanctions.
In a statement it said: “The Croatian Football Federation distances itself from all deviant behaviour of the part of the fans during the final tournament of UEFA Euro 2012 and strongly condemns it.
“The HNS, its national team players and members of the technical staff support all UEFA activities aimed at identifying individuals whose behaviour damages the reputation of the competition, no matter which country they come from.
“The HNS appeals to UEFA not to punish the Croatian national team, which is for a number of years at the top of world football because of its performances and behaviour, both on and off the field of play, and not to associate it with the part of the fans who actually are not supporters, but hooligans which should be isolated from all sports events.”
Croatia were fined $25,000 by FIFA just under four years ago after England striker Emile Heskey was subjected to monkey chants in a World Cup qualifier in Zagreb.
They were also given a small fine during Euro 2008 for racist abuse from their fans during their game against Turkey.
Alleged racist chanting in the Spain-Italy and Russia-Czech Republic games are already subject to investigations.
A Spanish fans’ group has said some of its country’s supporters abused striker Mario Balotelli in their game with Italy, while Czech Republic defender Theodor Gebre Selassie told reporters he “noticed” racist chants directed at him.
Mario Balotelli, who started the 1-1 draw against Croatia, said before Euro 2012 that he would “not accept racism at all” and would walk off the pitch if racially abused by fans.
Netherlands players said they heard racist chanting during a pre-tournament open training session in Krakow.
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