Milosevic, who suffered chronic heart ailments and high blood pressure, apparently died of natural causes and was found in his bed, the U.N. tribunal said, without giving an exact time of death.
He had been examined following frequent complaints of fatigue or ill health that delayed his trial, but the tribunal could not immediately say when his last medical checkup was. All detainees at the center in Scheveningen are checked by a guard every half hour.
The tribunal said Milosevic's family had been informed of his death, which came nearly five years after he was arrested, then extradited to The Hague.
Chief U.N. war crimes prosecutor Carla Del Ponte said she regretted Milosevic's death because she believed she would have won his conviction.
"I also regret it for the victims, the thousands of victims, who have been waiting for justice," Del Ponte told German-language Swiss Television DRS while visiting her native Switzerland.
His wife, Mirjana Markovic, who was often accused of being the power behind the scenes during her husband's autocratic rule, has been in self-imposed exile in Russia since 2003. His son, Marko, also lives in Russia, and his daughter, Marija, lives in Montenegro. Milosevic was regularly visited by his wife and other family members.
Borislav Milosevic, who lives in Moscow, blamed the U.N tribunal for causing his younger brother's death by refusing him medical treatment in Russia.
"All responsibility for this lies on the shoulders of the international tribunal. He asked for treatment several months ago, they knew this," he told The Associated Press. "They drove him to this as they didn't want to let him out alive."
Milosevic asked the court in December to let him go to Moscow for treatment. But the tribunal refused, despite assurances from Russia that Milosevic would return to finish his trial.
The White House said it was waiting for more information.
"We have seen the news that Slobodan Milosevic has died in his prison in The Hague," spokesman Blair Jones said. "We do not have all the details yet."
U.S. State Department acting spokesman Tom Casey said "the tribunal will be looking into the circumstances" of Milosevic's death.
The tribunal said it would conduct a full inquiry, including an autopsy on Sunday and toxicological examination. A pathologist from Serbia-Montenegro will observe the autopsy.
But Borislav Milosevic said his family does not trust the U.N. tribunal to conduct that autopsy impartially.
Slobodan Milosevic has been on trial since February 2002, defending himself against 66 counts of crimes, including genocide, in Croatia, Bosnia and Kosovo. He was the first sitting head of state ever to be indicted for such crimes.
He was accused of orchestrating a brutal campaign of ethnic cleansing against non-Serbs during the collapse of the Yugoslav federation — his attempt to link Serbia with Serb-dominated areas of Croatia and Bosnia to create a new Greater Serbia.
Supporters in Milosevic's homeland declared his death a "huge loss," while citizens of Bosnia, Croatia and Kosovo said his death brought some justice to his victims.
"Finally, we have some reason to smile. God is fair," said Hajra Catic, who heads an association of women that lost their loved ones in the 1995 massacre of 8,000 Muslims in the eastern Srebrenica enclave by Serb troops.