Dr. Boles's final Ph.D. student graduated in 2018. His final year of teaching was 2018-2019.
- Jefferson: Architect of American Liberty (Basic Books, 2017).
- Seeing Jefferson Anew In His Time and Ours, co-edited with Randal L. Hall (University of Virginia Press, 2010).
- University Builder: Edgar Odell Lovett and the Founding of the Rice Institute (LSU Press, 2007).
- A Companion to the American South (Blackwell, 2007).
- The South Through Time: A History of an American Region, rev. (Prentice Hall, 2004).
- A University So Conceived: A Brief History of Rice, rev. (Rice University Press, 1997).
- Black Southerners, 1619 -1869 (University Press of Kentucky, 1984).
- The Great Revival, 1787-1805: The Originals of the Southern Evangelical Mind (University Press of Kentucky, 1972).