Following the dissolution of the Soviet Union during the first years of the 1990s, sensitive archives in Russia began to tentatively be opened to scholars. In 1993, in his capacity with the Manuscript Division of the Library of Congress, Haynes became the first American scholar to examine the records of the Communist Party USA, housed in the former archive of the Communist International in Moscow.[3]
Haynes was later instrumental in helping to forge a December 1998 agreement between the institutional forerunner of today's Russian State Archive of Socio-Political History (RGASPI), keeper of the Comintern documents, and the Library of Congress which led to the microfilming of the CPUSA collection and its sale to academic institutions.[3]
Pseudonyms of Authors: Including Anonyms and Initialisms. Detroit: Gale Research Co., 1969. OCLC 642930477.
"The 'Rank and File Movement" in Private Social Work," Labor History, vol. 16, no. 1 (Winter 1975).
Liberals, Communists, and the Popular Front in Minnesota : The Struggle to Control the Political Direction of the Labor Movement and Organized Liberalism, 1936-1950. PhD dissertation. University of Minnesota, 1978.
Dubious Alliance: The Making of Minnesota's DFL Party. Minneapolis, MN: University of Minnesota Press, 1984. OCLC 10072296.
Communism and Anti-Communism in the United States: An Annotated Guide to Historical Writings. New York: Garland, 1987. OCLC 14413516.
"The Cold War Debate Continues: A Traditionalist View of Historical Writing on Domestic Communism and Anti-Communism," Journal of Cold War Studies, vol. 2, no. 1 (Winter 2000), pp. 76–115. OCLC 90637039.
In Denial: Historians, Communism and Espionage. With Harvey Klehr. San Francisco: Encounter Books, 2003. OCLC 62271849.
Early Cold War Spies: The Espionage Trials that Shaped American Politics. With Harvey Klehr. New York: Cambridge University Press, 2006. OCLC 63171119.
Spies: The Rise and Fall of the KGB in America. With Harvey Klehr and Alexander Vassiliev. New Haven, CT: Yale University Press, 2009. OCLC 262432345.
Secret Cables of the Comintern, 1933-1943. With Fridrikh Igorevich Firsov and Harvey Klehr. New Haven, CT: Yale University Press, 2014. OCLC 861955213.
Victoria Phillips, "Reflections of a Neo-Liberal: An Interview with John Haynes," American Communist History, vol. 13, no. 2-3 (Aug.-Dec. 2014), pp. 85–151.