President Boris Tadic has become the first Serbian leader to pay his respects to Croatian victims of a notorious 1991 massacre.
During a visit to a memorial to 260 people murdered at Vukovar, Mr Tadic gave a statement expressing his "apology and regret".
Vukovar was captured in November 1991 after a three-month siege by the Serb-led Yugoslav army.
The victims of the massacre had sought refuge in the town's hospital.
But two days after Vukovar was seized, they were led to the site of a pig farm and shot, their bodies left in a mass grave.
Mr Tadic arrived in Vukovar on a ferry which crossed the Danube from the Serbian town of Bac.
He was welcomed by Croatian President Ivo Josipovic, and a crowd of around 50 people.
The two men went together to the memorial at Ovcara and laid wreaths at the site of the mass grave.
Mr Tadic said he had come to bow down before the victims to open the way for forgiveness and reconciliation.
"I came here to share words of apology; to express our sympathy; to create the possibility for Serbs and Croats, Serbia and Croatia, to turn a new page in history," he said.
The Croatian president promised that no crimes committed at the time would go unpunished.
"We will finish this process of reconciliation and Serbia and Croatia will be two friendly, neighbouring countries," he said.
They later laid wreaths in the village of Paulin Dvor where 18 Serbs and an ethnic Hungarian were killed by Croatian forces in December 1991.
Croatia has described the event as an attempt to relax relations between the two countries.
But a number of Croatian right-wing parties and war veteran groups have objected to the visit.
Several mothers of people killed in Vukovar attended the wreath-laying ceremony and turned their backs on Boris Tadic as he spoke.
The Hina news agency reported that protests took place in several cities and dozens of members of the right-wing Croatian Party of Rights lit candles in the centre of Zagreb to remember the victims of Vukovar.
More than 1,000 civilians died during the battle for the town. After it fell, 22,000 non-Serbs were expelled. More than 400 people from the town are still listed as missing.
Earlier this year, the Serbian president went to Bosnia to commemorate more than 8,000 Muslim men and boys killed by Serb forces at Srebrenica in 1995.
Our Balkans correspondent says both presidents are facing their nations' difficult past in an attempt to move towards a stable future, with the aim of membership of the European Union.
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