European football's governing body has already sanctioned the Russian FA for the displaying of "illicit banners" by their fans at the tournament, but the Croatians are the first to face disciplinary proceedings for racist chants and displaying racist symbols.
UEFA are still investigating reports of alleged racist chanting during Italy's match against Spain in Gdansk on June 10, and Russia's match with the Czech Republic in Wroclaw on June 8 - the opening day of the tournament.
The issue of racism dominated the build-up to the tournament, co-hosted by Poland and Ukraine and the biggest sporting event in Eastern Europe since the end of communism.
"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," UEFA said in a statement on Saturday.
UEFA is also investigating reports that a banana was thrown on to the pitch during the match which ended in a 1-1 draw.
The Football Against Racism in Europe (FARE) network, which works closely with UEFA and has two "international monitors" at each Euro 2012 game, tweeted on Friday that's its observers reported "between 300 and 500 Croatian fans were involved in racially abusing Italy striker Mario Balotelli".
The UEFA Control and Disciplinary Body will deal with the case on Tuesday.
The controversial Balotelli said before the tournament he would "kill" anyone who threw bananas at him in the street or walk off the pitch if he heard monkey noises during a match.
Czech defender Theodor Gebre Selassie, the first black player to be play for the Czech national team, said he had "noticed" racist chants directed at him during his side's game with Russia.
Some members of the Netherlands squad also complained of hearing monkey noises at an open training session at Wisla Krakow's stadium on June 8 when tens of thousands of Poles turned up to watch.