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- Steeltown, USSR: Soviet society in the Gorbachev era, University of California Press, 1991.
- Magnetic mountain: Stalinism as a civilization, University of California Press, 1995.
- Armageddon averted: the Soviet collapse, 1970-2000, Oxford University Press, 2001.
- Uncivil society: 1989 and the implosion of the communist establishment, Modern Library, 2009.
- Rediscovering Russia in Asia: Siberia and the Russian Far East, edited by Stephen Kotkin and David Wolff, M. E. Sharpe, 1995.
- Mongolia in the twentieth century: landlocked cosmopolitan, edited b y Stephen Kotkin and Bruce Elleman, M. E. Sharpe, 1999.
- Political corruption in transition: a skeptic's handbook, edited by Stephen Kotkin and András Sajó, Central European University Press, 2002.
- The cultural gradient: the transmission of ideas in Europe, 1789-1991, edited by Catherine Evtuhov and Stephen Kotkin, Rowman & Littlefield, 2003.
- Manchurian railways and the opening of China: an international history, edited by Bruce A. Elleman and Stephen Kotkin, M.. Sharpe, 2010.