During the hearing at the International Criminal Tribunal for the former Yugoslavia (ICTY), the prosecution said it wanted to amend the indictment but gave no further details.
Mr Karadzic, who appeared in court shorn of the long hair and bushy beard he grew while on the run, said he would want more time to study any new indictment.
When asked whether he had any issues to raise, Mr Karadzic said he wanted to inform the judge about irregularities about his transfer to tribunal. He said he had been seized and held by "unknown civilians" for three days before the official arrest date given to the court.
He said his rights were denied him - even the opportunity to telephone or text friends who may have been searching for him in hospitals or mortuaries.
Mr Karadzic wanted to read out a four-page speech which included details about an alleged deal with the former US ambassador to the United Nations Richard Holbrooke for him to withdraw from public and literary life.
Mr Karadzic said he had wanted to appear before the tribunal when first indicted in 1996 - but was in fear of being "liquidated" if he did so, under the terms of the "deal".
The judge stopped him and said these were not matters for the initial hearing and he would get ample opportunity to explain them to the tribunal.
Mr Holbrooke later told the BBC that Mr Karadzic's claims were "laughably ludicrous".
He said it was hilarious and one could sense the desperation in his voice, the phoney details and total invention it represented. There was never any deal to prevent Mr Karadzic's capture, Nato just failed to capture him, Mr Holbrooke added.
He said he hoped Mr Karadzic's army chief Ratko Mladic would also be caught and brought to justice.
Correspondents say Mr Karadzic's sensational claims and his decision to conduct his own defence means this first court appearance is likely to be just the opening skirmish in a long legal battle.
The world is looking at this as if it were a spectacle
Kada Hotic Relative of victim
The BBC's Helen Fawkes in Belgrade said there had been a mixed reaction to the hearing.
One man said that as Mr Karadzic was a Serb, he had been convicted before trial started. But another told our correspondent the trial heralded a new start for Serbia.
Some relatives of the victims of the Bosnian war watched the hearing on television.
Kada Hotic, whose son was killed when Serb troops overran Srebrenica said the hearing was "theatre".
"He stole the ground from under our feet and he took the sky from above our heads, he killed our sons," she told the AFP news agency.
"And what we get in return is a theatre performance. The world is looking at this as if it were a spectacle."
The Muslim member of Bosnia's tri-partite presidency, Dr Haris Silajdzic, told the BBC's Arabic Service that putting Mr Karadzic on trial was not enough.
He said the conditions and ideology that surrounded Mr Karadzic were still alive and in evidence.
"Radovan Karadzic established the Serbian republic in Bosnia and Hercegovina based on genocide, collective displacement, ethnic cleansing and so on," he said.
"What would satisfy people in Bosnia and Hercegovina as well as international justice... is to see the constitution of Bosnia and Herzegovina amended, and to overcome the consequences of genocide."
Serbian officials say Mr Karadzic was arrested on 21 July in Belgrade. He had changed his appearance and was working as an alternative therapist.
Karadzic's daughter and wife will now receive passports
He was transferred to The Hague on Wednesday hours after clashes at a rally attended by at least 10,000 supporters to protest about his arrest.
The 63-year-old had reportedly attempted to challenge the legality of his transfer, but a senior member of his legal team has now told the BBC that no appeal was ever lodged.
However, a travel ban on his family was lifted on Wednesday, to allow them to visit him in The Hague.
Their documents had been confiscated in January under suspicion that they were helping Mr Karadzic in hiding.
Mr Karadzic led the formation of a separate Bosnian Serb assembly in 1991 - one of the sparks that ignited the 1992-1995 Bosnian war.
As well as the charges he faces over Srebrenica and Sarajevo, he is also accused of using 284 UN peacekeepers as human shields in May and June 1995.
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