The career of Mr Waldheim, who headed the UN from 1972 to 1982, was overshadowed by a scandal about his secretive World War II service.
Despite allegations he belonged to a German army unit that committed atrocities in the Balkans, he was elected Austria's president in 1986.
Admitted to hospital in Vienna last month, he died of heart failure.
Initial denial
The allegations arose in 1986, shortly after his nomination for the role of Austrian president.
"Day after day, I have been relentlessly pursued over events which happened 40 or more years ago"
The World Jewish Congress claimed he had been an officer attached to a German Army command which sent more than 42,000 Greek Jews from Salonika to their deaths, and was responsible for the massacre of thousands of Yugoslavs in the Kozara mountains.
Mr Waldheim's initial denial of the allegations - followed by his subsequent assertion that he was only doing his duty - caused international outrage.
"Day after day, I have been relentlessly pursued over events which happened 40 or more years ago," he said during an interview in 1988.
"My enemies kept bringing up new charges against me and promising new evidence. But this evidence never appeared."
Murder plot
Many Austrians did not believe the accusations against the man they elected president.
But they sparked international censure. The US, for example, banned him from visiting the country.
Later, Mr Waldheim said that the scandal surrounding his presidency forced Austrians to admit that they were not all passive victims of Nazi Germany.
During his time as UN Secretary General, Mr Waldheim flew to Iran in a vain attempt to negotiate the release of the US hostages held in Tehran. But Ayatollah Khomeini refused to see him.
While in Tehran, it was announced that a plot to kill Mr Waldheim had been foiled.
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