The tribunal will "ensure his well being and right to a fair trial as much as possible and in accordance with the highest international standards," spokeswoman Nerma Jelacic said in confirming Karadzic's arrival at the detention center outside The Hague.
Prosecutors allege Karadzic masterminded atrocities including the 1995 massacre of 8,000 Muslim men and boys in the Bosnian town of Srebrenica, the deadly siege of Sarajevo, and the detention of tens of thousands of people in 20 concentration camps where many were tortured, starved and sexually abused.
The court announced he will be summoned before a judge Thursday afternoon, where he will be asked to enter pleas on each of the 11 counts against him, including genocide, extermination and persecution.
Karadzic's lawyer, Svetozar Vujacic, said his client will postpone entering a formal plea for 30 days, the maximum allowed under court rules.
It is likely to be several months before his trial begins, and it could last several years.
Chief prosecutor Serge Brammertz scheduled a news conference for later Wednesday.
Vujacic, speaking from Belgrade, acknowledged he never filed an appeal against Karadzic's extradition from Serbia. The lawyer previously claimed he sent an appeal by registered mail from Bosnia before a midnight deadline on Friday.
The uncertainty over the appeal helped stall Karadzic's handover, Vujacic said.
The tribunal declined to give details of Karadzic's transfer to The Hague, citing security in future cases. But the confirmation of his arrival came shortly after a helicopter landed behind the high wall of the jail while another helicopter hovered overhead. Two black minivans drove through the prison gates moments earlier.
Hours before masked drivers whisked Karadzic to Belgrade's airport early Wednesday, about 15,000 Serb extremists rallied in a main square in the Serbian capital, demanding a halt to the extradition. Several hundred hooligans separated from the group and hurled stones and burning flares at riot police.
Later, police fired tear gas and rubber bullets at large groups of demonstrators, trying to push them away from the square as the rally ended. Belgrade's emergency clinic reported 46 people injured, including 25 policemen and 21 civilians. Most were lightly injured, doctors said, adding that only one civilian and one policeman were hospitalized.
Streets looked like battlefields, with smashed shop windows and overturned garbage cans. Ambulance sirens blared through downtown. Police Chief Milorad Veljovic said the area was "under control" by midnight.
Legal experts consider Karadzic the most important figure in the war crimes committed in Bosnia, exceeding the role played by the late Yugoslav President Slobodan Milosevic, whose own trial ended inconclusively when he died in 2006 in the same U.N. jail.
Karadzic's top commander, Ratko Mladic, also accused of genocide, remains at large.
Serbian authorities say they arrested Karadzic July 21 in Belgrade, where he had been living under a false identity and practicing alternative medicine. His bouffant mane of salt and pepper hair — his trademark during the Bosnian war — had gone, replaced by flowing white hair and a beard that drew comparisons with Santa Claus and Russian mystic Rasputin.
Since his capture Karadzic has asked for and gotten a shave and a haircut and his lawyer says he looks like an older version of the Bosnian Serb leader who regularly met with top Western officials, diplomats and military commanders during the 1992-95 Bosnian war.
During the war, he was known as the urbane, intellectual face of a monstrous regime blamed for the worst atrocities in Europe since World War II.
Prosecutors allege that the one-time psychiatrist and poet transformed himself into an ultranationalist Serb warlord before and during the war.
According to his indictment, Karadzic and other senior Bosnian Serb leaders unleashed a reign of terror that began with vicious campaigns of ethnic cleansing to drive Muslims and Croats out of land he considered part of a "Greater Serbia" and reached its bloody climax in the Srebrenica killings.
Serbia's new, pro-Western government hopes Karadzic's arrest will strengthen the country's bid for membership in the European Union. Serbia had been accused of not searching for war crimes fugitives sought by the U.N. tribunal.
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