"Participation in the public debate has become a dangerous activity. If you give your opinion, you risk being prosecuted," he said.
The three judges said that they had weighed Mr Wilders's "one-sided generalisations" against his right to free speech, and ruled that he had gone beyond the normal leeway granted to politicians.
In March 2008, Mr Wilders posted a film about the Koran on the internet, prompting angry protests across the Muslim World.
The opening scenes of Fitna - a Koranic term sometimes translated as "strife" - show a copy of the holy book followed by footage of the bomb attacks on the US on 11 September 2001, London in July 2005 and Madrid in March 2004.
Dutch Prime Minister Jan Peter Balkenende said at the time that the film wrongly equated Islam with violence and served "no purpose other than to offend".