Milosevic does not recognise the UN tribunal
The charges against the former Yugoslav president include genocide and war crimes.
The trial is expected to be one of the most complex cases in post-war legal history.
'Master plan'
The prosecution had argued in favour of a single trial on the basis that witnesses would have to testify only once.
Chief Prosecutor Carla Del Ponte has also stressed that a single trial will benefit the victims and their families.
"It is very important for the victims to have a single trial because they can hear all the facts in the same procedure and see justice done at the same time," she was quoted as saying.
The prosecution successfully argued that Mr Milosevic's alleged crimes in all three conflicts were part of a master plan to create a Greater Serbia.
Mr Milosevic has said he does not recognise the legitimacy of the UN tribunal or the charges against him.
"By adding up three lies you will not get to the truth, you will enlarge the lie," he said during Wednesday's hearing on whether to hold a single trial.
Mammoth task
Mr Milosevic faces a total of 66 counts of crimes against humanity, violating the laws and regulations of war, and genocide.
If found guilty, he could face life imprisonment.
The trial, which has been compared in scale to the Nuremberg trials which followed the end of World War II, could last several years.
Prosecutors have said they will call up to 30 political insiders to give evidence linking Mr Milosevic to the atrocities of the wars in Bosnia, Croatia and Kosovo.
But some reports have cast doubt on whether the prosecution has enough witnesses to make its case after key political figures in Serbia denied they would appear.
The prosecution may also have difficulties in presenting material evidence, as Serbian forces are reported to have destroyed proof of their atrocities.