Amano, who last went to Tehran in November, is due to hold talks with Iranian leaders and senior officials, the IAEA said.
"The visit is part of the efforts to advance dialogue and cooperation between the agency and Iran," it said.
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A spokesman for lead negotiator Catherine Ashton, the EU's foreign policy chief, had said earlier this month that the negotiations would take place before the UN General Assembly, which starts on September 16.
After several months of talks, Iran and the five permanent members of the UN Security Council plus Germany decided last month to extend their self-imposed deadline of July 20 to strike an agreement until November 24.
Such an accord is aimed at easing fears once and for all that the Islamic republic might use its civilian nuclear programme to build an atomic bomb, something Tehran has always denied.
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