In 1983, Middlekauff became the President of Huntington Library, Art Collections and Botanical Gardens in San Marino, California, until 1987.
Middlekauff is best known for The Glorious Cause, a history of the American Revolutionary War. He was the Harold Vyvyan Harmsworth Professor of American History in 1996-7.
- Ancients and Axioms: Secondary Education in Eighteenth-Century New England (New Haven: Yale University Press, 1963).
- The Mathers: Three Generations of Puritan Intellectuals, 1596-1728, winner of the Bancroft Prize. (Oxford: Oxford University Press, 1971) reprinted in paperback (Berkeley: University of California Press, 1999).
- The Glorious Cause: The American Revolution, 1763-1789 (Oxford: Oxford University Press, 1982, paperback ed., 1986) (Revised and Expanded Edition, 2005, ISBN 978-0-19-516247-9).
- Benjamin Franklin and His Enemies (Berkeley: University of California Press, 1996; paperback ed., 1998).
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