Karadzic, who was arrested by Serbian security forces last week after more than a decade in hiding, arrived in the Netherlands on Wednesday morning and is being held in UN custody at a detention center.
Karadzic, 63, will be tried for his role in the 1992-95 Bosnia war, including the massacre of 8,000 Bosnian Muslims at Srebrenica in 1995 and the siege of Sarajevo, during which 10,000 people died.
At Thursday's hearing, Karadzic will have the chance to enter a plea. He is expected to plead not guilty.
Karadzic also has the right to choose a lawyer. His current lawyer, Svetozar Vujacic, said last week that Karadzic would defend himself at the UN tribunal in The Hague. However, the judges may dismiss Vujacic and appoint another lawyer.
Chief Prosecutor Serge Brammertz told reporters in The Hague that Karadzic's trail would start in the next few months.
Mikhail Margelov, who heads the international affairs committee in the upper house of Russia's parliament, has expressed the hope that the Hague tribunal would refrain from double standards at the trial.
"I wish the Hague tribunal would avoid double standards at the trial of Karadzic, passing an unbiased judgment on the action of all sides in the conflict, be they Bosnians, Kosovo Albanians or Serbs," the Federation Council member said Wednesday.
Although Karadzic's arrest is expected to facilitate accession to the European Union for Serbia, the event provoked protests in Belgrade.
Around 16,000 Serb nationalists, who consider Karadzic a national hero, held a mass rally in central Belgrade on Tuesday night. Protestors led by the Radical Party with the support of the Democratic Party of Serbia accused Serbia's pro-Western President Boris Tadic and his government of betraying the country's interests in extraditing Karadzic.
The protests gradually turned violent. Nationalists hurled rocks, Molotov cocktails, garbage and firecrackers at riot police. The latest reports said 80 people, including 54 police officers, were injured. Several shop windows were smashed during the violence.
