Dr. Haefeli's research has ranged from the frontier between New France and New England, to early Native American history, the famous Salem witchcraft trials, obscure revolts in colonial New York, captivity narratives and the nature of book publishing in colonial America, and the politics of religious toleration in the Dutch empire, especially New Netherland.
- Haefeli, E. (2007). On first contact and apotheosis: Manitou and men in North America. Ethnohistory. 54(3), 407-443.
- Haefeli, E. (2006). The revolt of the long Swede: Transatlantic hopes and fears on the Delaware, 1669. Pennsylvania Magazine of History and Biography. 130(2), 137-180.
- Haefeli, E., & Sweeney, K. (2004). The redeemed captive as recurrent seller: Politics and publication, 1707-1853. The New England Quarterly. 77(3), 341-366.
- Haefeli, E. (1999). A note on the use of North American Borderlands. AMERICAN HISTORICAL REVIEW. 104(4), 1222-1225.
- Haefeli, E. (2013). New Netherland and the Dutch origins of American religious liberty.
- Haefeli, E., & Sweeney, K. (2006). Captive histories: English, French, and native narratives of the 1704 deerfield raid.
- Haefeli, E. (2015). How Special was Rhode Island? The Global Context of the 1663 Charter. Beneke, C., & Grenda, C. S. (Eds.), The Lively Experiment Religious Toleration in America from Roger Williams to the Present. (pp. 21-36). Rowman & Littlefield.
- Haefeli, E. (2015). The Problem with the History of Toleration. Sullivan, W. F., Hurd, E. S., Mahmood, S., & Danchin, P. G. (Eds.), Politics of Religious Freedom. (pp. 105-114). University of Chicago Press.
- Haefeli, E. (2013). Breaking the Christian Atlantic: The legacy of Dutch tolerance in Brazil. van Groesen, M. (Eds.), The Legacy of Dutch Brazil. (pp. 124-145). Cambridge University Press.
- Foster, S., & Haefeli, E. (2013). British North America in the Empire: An Overview. Foster, S. (Eds.), British North America in the Seventeenth and Eighteenth Centuries. (pp. 18-66). Oxford University Press.
- Haefeli, E. (2013). Laurentius van den Bosch, (c.1660? 1696). van den Broeke, L., Krabbendam, H., & Mouw, D. (Eds.), Transatlantic Pieties Dutch Clergy in Colonial America. (pp. 217-235). Wm. B. Eerdmans Publishing Company.
- Haefeli, E., & Stanwood, O. (2006). Jesuits, Huguenots, and the apocalypse: The origins of America's first French book. Proceedings of the American Antiquarian Society. 116(1), 59-119.