The film, in which director Péter Vadócz finds the flags of all of the European Union member states in ordinary places in Hungary, has been in competition at more than 120 festivals. The special mention was its 13th acknowledgement.
Colorful EU will be shown in New York's Times Square with the other prize winners on December 17.
The chairman of the jury for Metropolis Art Prize 2009 was Isabella Rossellini.