During his presidential term in Austria, documents surfaced showing Waldheim had served in the Nazi Brownshirts, a paramilitary force, prior to World War II. He had later served under General Alexander Lohr, who was executed for war crimes in 1947. Further allegations surfaced showing Waldheim took part in a German raid on Yugoslavia , Operation Kozara , where thousands of civilians were killed as part of a "cleansing" campaign. Documents came to light in the mid 1980's that in 1948 the U.N. War Crimes Commission reached a secret finding stating there was sufficient evidence to prosecute Waldheim for "murder" and "putting hostages to death."
Waldheim's term at the U.N. was viewed with contempt by most of the world powers. American diplomats saw him as largely uncooperative due to his penchant to avoid controversy. Waldheim had led a U.N. diplomatic mission to Iran to moderate the American hostage crisis there in 1979. He, and his U.N. team, fled the country in face of violent protests by Iranians.
Waldheim had stated that intelligence agencies of world powers were aware of his involvement in Hitler's regime. Though he made no mounted efforts to clear his name, there has been no evidence suggesting that he had directly participated in war crimes.