Iranian nuclear physicist Shahram Amiri has left the United States for Iran, Iranian Foreign Ministry spokesman Ramin Mehmanaparast was quoted as saying by the Mehr news agency.
He added that Amiri's return was made possible through cooperation with the Pakistani Embassy in Washington.
Amiri disappeared during his Hajj in Saudi Arabia in spring 2009.
According to international media, 30-year-old Amiri, who worked at a secret Iranian nuclear facility for three years, is one of the country's most knowledgeable young nuclear physicists.
Tehran has accused U.S. intelligence agencies of kidnapping Amiri.
In early June, Iranian television channels broadcast footage supporting these accusations, which stated that the scientist was being held in the city of Tucson, Arizona.
Prior to his kidnapping, Amiri worked at the Tehran University of Technology "as a private specialist." Tehran denies his involvement in the Iranian nuclear program.
Later Western media reported that the Iranian scientist himself decided not to return to Iran and began cooperating with U.S. intelligence agencies.
In early December 2009, the British weekly Sunday Telegraph reported that Amiri met with IAEA inspectors at a Frankfurt airport in October and provided "extremely useful" data.