From Citizendium, the Citizens' Compendium
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- The Puritan Family (1942)
- Virginians at Home: Family Life in the Eighteenth Century (1952)
- The Stamp Act Crisis: Prologue to Revolution (1953), with Helen M. Morgan,
- The Birth of the Republic, 1763-89 (1956), short survey
- The Puritan Dilemma: The Story of John Winthrop (1958)
- The American Revolution: A Review of Changing Interpretations (1958), short pamphlet
- The Mirror of the Indian: An Exhibition of Books and Other Source Materials (1958), 57pp guide to exhibit
- Editor, Prologue to the Revolution: Sources and Documents on the Stamp Act Crisis, 1764-1766 (1959)
- The National Experience: A History of the United States (1963) coauthor of colonial and Revolution sections of this college textbook; several editions to 1989
- Visible Saints: The History of a Puritan Idea (1963)
- Editor, The Founding of Massachusetts: Historians and the Sources (1964)
- The American Revolution: Two Centuries of Interpretation (1965), short pamphlet
- ed. Puritan Political Ideas, 1558-1794 (1965)
- ed. The Diary of Michael Wigglesworth, 1653-1657: The Conscience of a Puritan (1965)
- Roger Williams: The Church and the State (1967)
- American Slavery, American Freedom: The Ordeal of Colonial Virginia (1975), highly influential study.
- The Challenge of the American Revolution. New York: W. W. Norton, 1976. [Collection of essays.]
- The Meaning of Independence: John Adams, George Washington, and Thomas Jefferson (1976).
- The Genius of George Washington (1980).
- The Gentle Puritan: A Life of Ezra Stiles, 1727-1795 (1984)
- Inventing the People: The Rise of Popular Sovereignty in England and America (1988).
- Benjamin Franklin (2002).
- The Genuine Article: A Historian Looks at Early America (2004), collected articles and reviews.
- "The Historians of Early New England." In The Reinterpretation of Early American History: Essays in Honor of John Edwin Pomfret, 41-63. Ed. by Ray Allen Billington. San Marino, Calif.: The Huntington Library, 1966.
- “Slavery and Freedom: The American Paradox,” The Journal of American History, 59 (Jun., 1972), 5-29.
- Courtwright, David T. "Fifty Years of American History: An Interview with Edmund S. Morgan," The William and Mary Quarterly, 3rd Ser., Vol. 44, No. 2 (April 1987): 336-369.
- Murrin, John M. "Edmund S. Morgan," in Robert Allen Rutland, ed. Clio's Favorites: Leading Historians of the United States, 1945-2000, 126-137. Columbia: University of Missouri Press, 2000.
- New York Times obituary, July 9, 2013.