Before joining as a senior fellow at the Belfer Center for Science and International Affairs, Harvard Kennedy School of Government, Heinonen spent 27 years at the International Atomic Energy Agency in Vienna. Heinonen served the last five years as Deputy Director General of the IAEA and the head of its Department of Safeguards. He led the agency's efforts to identify and dismantle nuclear proliferation networks, including the one led by Pakistani scientist A. Q. Khan, and he oversaw its efforts to monitor and contain Iran's nuclear program. Heinonen led teams of international investigators to examine nuclear programs of concern around the world and inspected nuclear facilities in South Africa, Iraq, North Korea, Syria, Libya, and elsewhere, seeking to ensure that nuclear materials were not diverted for military purposes. He is considered one of the world's leading experts on Iran's nuclear program. He led the Agency's efforts in recent years to implement an analytical culture to guide and complement traditional verification activities.