It is not the first time mass graves from the conflict have been found in Serbia. The bodies of more than 800 Kosovo Albanians were found in several locations in Serbia in 2001, including police compounds.
The bodies were moved out of Kosovo before a Nato bombing campaign forced Serbian security forces out of the region.
Other, smaller mass graves have been found containing Serbian victims of ethnic Albanians.
Researchers in Serbia and Kosovo say more than 11,000 people died in the Kosovo conflict, most of them ethnic Albanian, but at least 2,300 Serbs.
A further 1,800 people are classified as missing, according to Eulex figures, but are presumed to be dead.
A former top Serbian police official, Vlastimir Djordjevic, is currently on trial at the UN's Hague-based war crimes tribunal for the former Yugoslovia.
Other mass graves of Kosovo Albanians have been found in Serbia
He was allegedly involved in the murders of hundreds of ethnic Albanians and the deportation of 800,000 others from Kosovo during the conflict, when he was in charge of police forces in Serbia.
He denies charges of deportation, murder and persecution.
He was a close aide to the late Yugoslav President Slobodan Milosevic, who died in tribunal custody in 2006 before a verdict was reached in his trial for war crimes.
Belgrade withdrew forces from the Serbian province of Kosovo in 1999 after a Nato bombing campaign, and the area was put under UN control.
Kosovo's declaration of independence in 2008 has been recognised by more than 50 countries, including the US and most EU states, but not recognised by more than 100, including Serbia and Russia.
Recent Serbian governments have been pro-Western and last year the country submitted a formal application to join the EU.
But membership negotiations cannot begin in earnest until two war crimes suspects - including the former Bosnian Serb military commander Ratko Mladic - have been captured.
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