Former Bosnian leader Radovan Karadzic was in a jail cell in the Netherlands on Wednesday after being taken there by plane in the middle of the night from Belgrade.

The plane believed to be carrying Karadzic arrived at an airport in Rotterdam, and then the 63-year-old captured war crimes fugitive was transferred to a cell in the UN detention centre on the edge of The Hague.

Bosnian Serb leader Radovan Karadzic is shown in a 1996 file photo, left, and in an undated photo, right, from Belgrade's Healthy Life magazine, a publication he contributed to. (Associated Press)

Thousands of hardline nationalists rallied to protest Karadzic's extradition before he was whisked away from the Serbian capital of Belgrade in a white government jet around 4 a.m. local time.

Karadzic's arrival in The Hague marks the end of a 13-year effort by the International Criminal Tribunal for the former Yugoslavia to take custody of its most wanted war criminal.

The psychiatrist-turned-politician is accused of orchestrating atrocities including the 1995 massacre of 8,000 Muslim men and boys, the deadly siege of Sarajevo and the detention of tens of thousands of people in concentration camps.

Karadzic is scheduled to make his first court appearance Thursday at 4 p.m. local time. He will be asked to enter pleas on each of the 11 counts against him, which include genocide, extermination and persecution.

His lawyer, Svetozar Vujacic, said his client intends to postpone entering a plea until the end of the 30 days allowed under court rules.

It will likely be several months before Karadzic's trial begins and the process could last several years.

'Serbian authorities deserve full credit'

Vujacic acknowledged Wednesday that he never filed an appeal against Karadzic's extradition as he claimed to have done by registered mail shortly before the midnight Friday deadline.

He said uncertainty over the appeal helped stall Karadzic's handover.

A helicopter believed to be carrying former Bosnian Serb leader Radovan Karadzic arrives at the detention unit of the Yugoslav war crimes tribunal, inside a maximum security Dutch prison in The Hague, Netherlands on Wednesday. (Ermindo Armino/ Associated Press)

Speaking at a press conference Wednesday in The Hague, Serge Brammertz, chief prosecutor for the International Criminal Tribunal for the former Yugoslavia, called Karadzic's arrest a "major achievement" of Serbia's co-operation with the tribunal.

"The Serbian authorities deserve full credit for the apprehension of Radovan Karadzic," said Brammertz.

He said the trial will be complex, but the tribunal plans to present the case in the "most efficient manner," saying lessons were learned from former Yugoslavian leader Slobodan Milosevic's lengthy, inconclusive trial.

Milosevic, Karadzic's mentor, died from a heart attack in 2006 before the tribunal reached a verdict on his charges of genocide and crimes against humanity after a years-long trial.

Brammertz also said he hopes Serbia's co-operation leads to the arrest of two remaining fugitives, needed to fulfil the mandate of the International Criminal Tribunal for former the Yugoslavia — wartime commander Ratko Mladic and former Croatian Serb political leader Goran Hadzic.

Nationalist rally turns violent

The announcement of Karadzic's extradition followed a violent nationalist rally on Tuesday, attended by thousands of Serbian hardliners who support Karadzic and are against the country's pro-Western government.

Belgrade's emergency clinic reported 46 people injured, including 25 policemen and 21 civilians, but doctors said no one appeared to have life-threatening wounds. Police estimated 15,000 people attended the rally.

Many Serbian extremists still regard Karadzic as a hero for helping to create a Serb ministate in Bosnia during the 1992-95 Balkan war.

Serbian authorities said they arrested Karadzic on July 21 in Belgrade where he had been living under a false name and practising alternative medicine.

The high-security prison where Karadzic is now held once housed Milosevic and currently has 37 accused Yugoslav war criminals behind its bars.

The war crimes tribunal jail is in a separate wing of a Dutch prison located in Scheveningen, a coastal suburb of The Hague.

With files from the Associated Press