The exhumation at the Rudnica quarry near the southwestern town of Raska was ordered after human remains were found in the area in December after more than three years of searching the site.
Dozens of experts were engaged in the process, which would last "until full investigation is done," said the chairman of Serbia's committee for missing persons, Veljko Odalovic.
Serbia's war crimes prosecutor Vladimir Vukcevic told AFP in 2010 that the grave might contain the remains of 250 Kosovo Albanians.
The quarry was one of the sites where forces under then-strongman Slobodan Milosevic moved civilians' remains from Kosovo at the end of the war, reburying them in Serbia in a bid to hide war crimes.
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More than 800 bodies of Kosovo Albanians were exhumed from three mass graves uncovered throughout Serbia in 2001.
Serbia's wartime deputy interior minister Vlastimir Djordjevic, sentenced by United Nations court for war crimes committed in Kosovo to 18 years in jail, is believed to have ordered the removal of ethnic Albanian victims and their reburial in mass graves in Serbia.
The conflict killed more than 13,000 people, mostly ethnic Albanians.
The war ended after a North Atlantic Treaty Organisation (NATO) bombing campaign in 1999 ousted Serb forces from the province, which was then put under United Nations administration.
Kosovo declared independence in 2008, a move recognised by the United States and most European Union member states but not by Belgrade.