Karadzic, dressed in a dark suit and tie, traced the origins of the 1992-95 war to the rejection by Bosnia's Muslim leadership of any power-sharing proposal.
He argued that conflicts resulting from the break-up of Yugoslavia were a natural consequence of the struggle for land.
Barnaby Phillips, Al Jazeera's correspondent in The Hague, said that Karadzic had appeared as "unapologetic, proud, at times even veering to sarcasm".
"Overall the tone of Mr Karadzic is proud, defiant, what he's saying is that there was certainly no plot on the part of the Bosnian Serbs to exterminate the Muslim, or Croat community," said Phillips.
"Certainly not to ethnically cleanse them out of any part of Bosnia.
"Rather the Serbs very reluctantly acquiesced in Bosnia's secession from Serbia, from Yugoslavia at that time, they didn't want that secession to happen.
"And even then it was Muslim desire for domination in Bosnia, and the nefarious interference of Western powers, perhaps in particular Germany, which took Bosnia into civil war, and not the acts of the Serbs themselves.
"It's an interesting defence, and it's a defence which I think will surprise many people in Western Europe and indeed in the Muslim world."
Addressing the court, Karadzic said: "I stand here before you not to defend the mere mortal that I am, but to defend the greatness of a small nation in Bosnia Herzegovina.
"Which for 500 years has had to suffer and has demonstrated a great deal of modesty and perseverance to survive in freedom."
The wartime Bosnian Serb leader is accused of having colluded with Slobodan Milosevic, the late Yugoslav leader, with the aim of creating a "Greater Serbia" that was to include 60 per cent of Bosnian territory.
Karadzic stands charged as the "supreme commander" of an ethnic cleansing campaign of Croats and Muslims in the Bosnian war in which 100,000 people were killed and 2.2 million displaced.
He is facing 11 counts of genocide, war crimes and crimes against humanity, but though he denies any wrongdoing, he has refused to enter a formal plea.
Among the charges against Karadzic are the 1995 Srebrenica massacre of more than 7,000 captured Muslim men and boys, and the 44-month siege of the capital Sarajevo that ended in November 1995, leaving about 10,000 people dead.
Hasan Nuhanovic, a survivor of the Srebrenica massacre who lost his parents and brother there, spoke to Al Jazeera from Sarajevo, the Bosnian capital.
Nuhanovic said: "Radovan Karadzic is being tried in The Hague, it's very important.
"But, it's even more important, in my opinion, that the shooters, the people who killed my family, who still live in my neighbourhood, not really far from where I live, they are still free. And they have not been prosecuted.
"So while their leader is being tried in The Hague, I expect the authorities of this country to try the war criminals who still live here in our neighbourhood, that's very important as well for this community."
Karadzic had refused to attend the opening of his trial last October, insisting on more time to prepare his case and causing a four-month delay.
Al Jazeera's Erica Wood reports on Karadzic's numerous efforts to delay his trial
He had sought a new delay of the trial until June 17 after his two-day opening statement concludes on Tuesday, to study an additional 400,000 pages of prosecution evidence he claims have been filed since October.
His request was refused by the court which ruled last Friday that the first prosecution witness, whose identity is being withheld, will testify on Wednesday.
Under these circumstances, Karadzic was likely to resume his boycott, said Marko Sladojevic, his legal adviser.
In November, the court appointed Richard Harvey, a British lawyer, to take over the defence if Karadzic opted to continue his boycott of the court.
First indicted in 1995, Karadzic eluded a Nato manhunt for more than a decade before being caught in July 2008 in Belgrade, where he had been living as a new-age philosopher.
Karadzic faces possible life imprisonment if convicted in what is one of the last and largest cases brought to the UN war crimes tribunal for the former Yugoslavia.
The UN Security Council, which set up the tribunal in 1993, has ordered it not to open new cases.
The tribunal has indicted 161 political and military officials, of which 40 cases are still continuing.
Two fugitives, Karadzic's former top general, Ratko Mladic, and Croatian Serb leader Goran Hadzic, could still be brought to trial at The Hague.
Karadzic is scheduled to return to the courtroom on Tuesday to present the rest of his opening statement.