Duffy is the author or editor of a number of books and articles. Her first policy report was "Power Politics: The Nuclear Industry and Nuclear Exports", with Gordon Adams, published by the Council on Economic Priorities in 1978, followed by "Soviet Nuclear Energy: Domestic and International Policies", published in 1979 by the Rand Corporation. This was followed by the textbook Blacker and Duffy, "International Arms Control Issues and Agreements", Stanford University Press, 1984 and Duffy, "et al." "Compliance and the Future of Arms Control", Ballinger, 1988. She has published articles in journals in her field such as "International Security", the "Bulletin of the Atomic Scientists", "Arms Control Today" and "Science" Magazine, and contributed chapters to many edited volumes on international security and foreign policy.