When he again failed to show the following day, the judge said the defendant had chosen not to exercise his right to be present and "must therefore accept the consequences", announcing the trial would proceed in his absence.
Judge Kwon has also said the court is considering imposing a lawyer to represent Mr Karadzic.
The defendant was the president of Republika Srpska, head of the Serbian Democratic Party (SDS) and commander of the Bosnian Serb Army during the 1992-1995 Bosnian War, which left more than 100,000 people dead.
He was indicted in 1995, and faces two charges of genocide and nine more of war crimes and crimes against humanity.
He was taken to the International Criminal Tribunal for the former Yugoslavia (ICTY) in The Hague last year, after 13 years in hiding.
Prosecutors say Mr Karadzic was the leader of an ethnic cleansing campaign in the Bosnian War, calling him the "undisputed leader" of Serbs responsible for carrying out atrocities during the conflict.
Prosecutors have said he is responsible for the Srebrenica massacre, in which up to 8,000 Bosniak men and boys were killed.
Mr Karadzic has not entered a plea, but is protesting his innocence.
He faces a maximum sentence of life in prison if convicted.
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