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The Serbian football team hung a flag depicting Kosovo in their dressing room before their World Cup match against Brazil, which they lost.
The Kosovo flag was filled with the Serbia flag with the words 'no surrender' written on it.
Tensions are running high between ethnic Serbs and the Albanian government in Kosovo.
Serbia does not see Kosovo as an independent country despite it declaring independence from Serbia in 2008.
The Kosovo Football Federation submitted a complaint to the world governing body of football.
In a statement, it said that such acts of chauvinism have no place in a sports event or in the facilities where the biggest event of world football takes place.
It said that it was unacceptable for this act to be passed in silence and requested that the football federation of Serbia be punished for their actions.
Kosovo's sports minister, Hajrulla Ceku, said it expected concrete actions from Fifa against Serbia.
Fifa's proceedings were opened on the basis of article 11 of theDisciplinary code, which is "offensive behavior and violation of the principles of fair play", and includes "using a sports event for demonstrations of a non-sporting nature".
Serbia and Kosovo can't play each other in World Cup qualification because of the tension between the two countries.
Serbia were beaten 2-0 by Brazil in their World Cup opener on Thursday, and will play another game on Monday.
Kosovo did not qualify for the tournament.
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