Worlds of Dissent: Charter 77, The Plastic People of the Universe, and Czech Culture under Communism (Harvard University Press, 2012).
- Winner of the Thomas J. Wilson Memorial Prize, Harvard University Press, for best first manuscript, 2010
- A Foreign Affairs Best Book on Eastern Europe and the Former Soviet Republics, 2012
- 2011–12 Aldo and Jeanne Scaglione Prize for Studies in Slavic Languages and Literatures, Modern Language Association
- Honorable Mention, Reginald Zelnik Book Prize in History, Association for Slavic, East European, and Eurasian Studies, 2012
- Honorable Mention, 2013 Book Prize, Czechoslovak Studies Association
- The Czech translation by Petruška Šustrová, Světy disentu: Charta 77, Plastic People of the Universe a česká kultura za komunismu (Praha: Academia, 2015), also includes my preface to the Czech edition.
- Reviewed in Wall Street Journal, Washington Post, Times Literary Supplement, Choice, Foreign Affairs, Frankfurter Allgemeine Zeitung, American Historical Review, Journal of Modern History, European History Quarterly, Nationalities Papers, Social History, Kritika, Slavic Review, Slavic and East European Journal, Bohemia, Zeitschrift für Ostmitteleuropa-Forschung, Central Europe, East Central Europe, Journal of Cold War Studies, Canadian Journal of History, Česká literatura, Český časopis historický, Dějiny - teorie - kritika, Střed, Lidové noviny, Respekt, Tvar, H7O, and elsewhere.
In the Puppet Gardens: Selected Poems 1963-2005, by Ivan Wernisch, edited and translated by Jonathan Bolton (Michigan Slavic Publications, 2007)
Nový historismus / New Historicism, ed. Jonathan Bolton (Brno: Host, 2007)
I have also written the afterword for Ludvík Vaculík's The Czech Dreambook, translated by Gerald Turner (Prague: Karolinum, 2020)