They were then dug up and reburied in more than 70 sites in an effort to cover up the extent of the killings.
The massacre has been designated an act of genocide by the UN's war crimes court and the international court of justice. It is remembered as the darkest day in the bloody break-up of the Yugoslav federation in the 1990s.
Struggling to recover
Sunday's memorial will be an emotional occasion for Srebrenica, which has struggled to recover from losing two generations of men and boys in the incident.
Hasan and Suhra Mahic, both in their eighties, will see their two sons Fuad and Suad buried during the service.
"I would have preferred that all of us have been killed together then we would not have had to live through this," Hasan said ahead of the ceremony.
Nearly 6,500 victims have been identified, but relatives of those still missing are hopeful that more bodies will be found in the dense woodland surrounding the town.
In a symbolic gesture of reconciliation, Boris Tadic, the Serbian president, will attend the ceremony, along with thousands of relatives of those who died.
Tadic said he hoped "to build bridges of friendship and understanding among nations in the region" by attending the ceremony.
Serbia has for years denied the scale of the crime and many Serbs, led by nationalist politicians, believe that allegations of genocide have been exaggerated as part of an international political conspiracy against the country.
But in March the country's parliament passed a declaration condemning the massacre and apologised to the victims and their families.
Al Jazeera's Barnaby Phillips reports on a Greek journalist who is being sued after claiming that Greeks were involved in the Srebrenica massacre.
General Ratko Mladic, the alleged mastermind of the killings, is still on the run and believed to be hiding in Serbia, where many see him as a heroic figure.
The other alleged architect of the massacre, Radovan Karadzic, was arrested in Belgrade in 2008, and is currently fighting charges of genocide, war crimes and crimes against humanity at the International Criminal Tribunal for the former Yugoslavia (ICTY).
The political party that he founded, the Serbian Democratic Party, chose to honour him on Saturday with a medal, saying it was not ashamed of the past.
UN peacekeepers were heavily criticised for allowing the massacre.
The Dutch troops tasked with protecting the town did not have the equipment or mandate to do so and allowed Bosnian Serb soldiers to take Muslim men and boys away after being assured they would not be harmed.