Choksy’s research broadly covers the development of societies, especially sectarian communities, in Central Asia, the Near East, and South Asia studied through interdisciplinary approaches involving history, religious studies, international affairs, politics, anthropology, archeology, language, literature, and numismatics. He focuses specifically on Iranian and Persian Studies, Indian subcontinental studies, Zoroastrianism, Islam, and Manichaeism. Choksy has conducted fieldwork in Iran, UAE, Pakistan, India, and Sri Lanka among other countries. Choksy is a frequent commentator in the media worldwide, with analyses appearing in Foreign Policy, World Politics Review, Real Clear World, Christian Science Monitor, National Review, NPR, Radio Liberty, Huffington Post, and ABC News among other policy journals and news media. He is a U.S. Presidentially-nominated and U.S. Congressionally-confirmed Member of the National Council on the Humanities which oversees the National Endowment for the Humanities in Washington, DC.