Accused war criminal Radovan Karadzic was extradited Wednesday morning from Serbia to the Netherlands where he will face genocide charges.

The former Bosnian Serb leader was captured almost two weeks ago after evading authorities for 13 years by changing his appearance and living a seemingly quiet, private existence as a health guru.

Just hours after a violent protest in Belgrade Tuesday night by thousands of his Serbian nationalist supporters, Karadzic was taken to a United Nations detention centre near The Hague to stand trial.

Karadzic will be brought before a judge on Thursday to enter a plea on 11 charges, including genocide and conspiracy to commit genocide, said former war crimes prosecutor Payam Akhavan.

"He can defer the plea for a period of 30 days. After that there will be a period of several months before the trial actually commences," Akhavan told CTV's Canada AM, reporting from Copenhagen, Denmark.

"The prosecution will have to be given a period of time to sift through what will be a mountain of evidence in order to prepare an effective defence."

Karadzic is still revered by many as a war hero for helping establish the Bosnian Serb mini-state.

About 15,000 of his supporters came out to protest his extradition on Tuesday, with most singing nationalist songs and waving posters of Karadzic.

The demonstration quickly turned violent, however as several hundred extremists threw stones and burning flares, clashing with police who retaliated with tear gas and rubber bullets.

In total, 46 people were reported injured, including 25 police and 21 civilians. Only one police officer and one civilian were hospitalized, however, with most of the injuries considered minor.

Akhavan said the demonstration represented a swan song of sorts for the radical nationalist faction, rather than an indication of how the country feels as a whole.

"The radicals received less than a third of the vote and although they boasted they would have 100,000 people at the rally there were only about 10,000. So I think it's not really a gauge of the popular mood."

Akhavan said there is likely a faction of nationalists who refuse to acknowledge the "terrible deeds that were committed in their name by their self-proclaimed nationalist saviour" but most have moved on.

"The vast majority of people voted in favour of the (Boris) Tadic government which is committed to European integration. For the radicals who are protesting it's more than anything a desperate dying convulsion and they have nothing to offer for the future of Serbia."

Neil MacDonald, a journalist with The Financial Times, told Canada AM that police were still on the streets Wednesday morning to guard against further violence.

"But the overall feeling is that the demonstration last night was maybe not a last gasp, but that it was the big statement by the nationalists and their political cause is in decline," MacDonald said.

Associated Press Television News footage showed a jet with Serbian markings landing at the Rotterdam airport Wednesday morning.

Less than an hour later, a helicopter landed inside the detention centre while another hovered overhead and two black minivans drove through the prison gates.

The Serbian government said it had issued a decree allowing Karadzic's extradition to face war crimes charges.

Among the charges against him Karadzic is accused of orchestrating the 1995 slaughter of 8,000 Muslim men and boys in the Bosnian city of Srebrenica.

He is also charged with spearheading the three-year siege of Sarajevo that resulted in the deaths of 10,000 people.