In his book American Sphinx: The Character of Thomas Jefferson (1996), Ellis explored the character and personality of Jefferson, and his many contradictions. He emphasized how important privacy was to him, and how the president and statesman preferred to work behind the scenes in politics, through letters, meetings and discussions over dinners. Ellis noted Jefferson's success in this style.
In relation to one of the major questions about his private life, whether Jefferson had a liaison with his slave "Sally Hemings, Ellis suggested that evidence was "inconclusive." His deep analysis of Jefferson's character led him to conclude that the statesman did not have the liaison. Specifically, Ellis says in the appendix to American Sphinx:
Unless the trustees of the "Thomas Jefferson Memorial Foundation decide to exhume the remains and do "DNA testing on Jefferson as well as some of his alleged progeny, it leaves the matter a mystery about which advocates on either side can freely speculate... This means that for those who demand an answer the only recourse is plausible conjecture, prefaced as it must be with profuse statements about the flimsy and wholly circumstantial character of the evidence. In that spirit, which we might call the spirit of responsible speculation, after five years mulling over the huge cache of evidence that does exist on the thought and character of the historical Jefferson, I have concluded that the likelihood of a liaison with Sally Hemings is remote.
On November 5, 1998, Dr. Eugene Foster and his team published the results of "Y-DNA analysis of Jefferson male-line descendants (he had no known male descendants but Y-DNA is passed on virtually unchanged through direct male-line descendants) and descendants of others reputed to be associated with him. Foster reported that DNA results showed a match between the Jefferson male line and the descendant of Eston Hemings. Given that and other historical evidence, they concluded that Thomas Jefferson was the father of Eston and probably of Sally Hemings' other children. The study showed no match between the Carr line, named by two of Jefferson's grandchildren as the father(s) of Hemings' children, and the Eston Hemings descendant, disproving the major alternative to Thomas Jefferson as father.
In interviews on "The NewsHour with Jim Lehrer in November 1998 and Frontline's Jefferson's Blood in 2000, Ellis made public statements about his change of opinion following the DNA studies, saying he believed that Jefferson had a long-term relationship with Sally Hemings.
In "His Excellency: George Washington (2004), Ellis sought to penetrate myth and examine Washington during three major periods of his life. Ellis described how Washington's experiences in earlier leadership contributed to his actions and development as president. Ellis wrote that "we do not need another epic [Washington biography], but rather a fresh portrait focused tightly on Washington's character", which the critic Jonathan Yardley said he had achieved.
False claims of combat service and anti-war leadership
In June 2001 the "Boston Globe revealed that Ellis had lied to his students in lectures and to the media about his role in American culture and the "Vietnam War years. He claimed to have been a combat platoon leader in Vietnam, to have been active in civil rights campaigns in the south, and to have been an anti-war leader at Yale. His actual military record consisted of obtaining a graduate student deferral of service until 1969 and then teaching history at "West Point until 1972. Ellis issued a public apology in August 2001 after the truth was exposed. In the ensuing controversy, Mount Holyoke suspended him without pay for a year, indefinitely suspended his status as an "endowed chair, and removed him from teaching during the 2001-2002 academic year. In May 2005, Mount Holyoke restored his chair.
- 1997 "National Book Award for Nonfiction, "American Sphinx: The Character of Thomas Jefferson
- 2001 "Pulitzer Prize for History, "Founding Brothers: The Revolutionary Generation 
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- Interview with Ellis on Passionate Sage: The Character and Legacy of John Adams, Booknotes, September 5, 1993, accessed February 16, 2012
- "Joseph Ellis: Putting History in Perspective". mountholyoke.edu. 2000. Retrieved 2006-08-04.
- Ellis, Joseph (1996). ""Appendix:Note on the Sally Hemings Scandal" From "American Sphinx", pp.303-307". pbs.org. Retrieved 2006-08-04.
- "Frontline: Jefferson's Blood: The History of a Story". Retrieved 2006-08-04.
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It's not so much a change of heart, but this is really new evidence. And it—prior to this evidence, I think it was a very difficult case to know and circumstantial on both sides, and, in part, because I got it wrong, I think I want to step forward and say this new evidence constitutes, well, evidence beyond any reasonable doubt that Jefferson had a longstanding sexual relationship with Sally Hemings. Even though the match is only with one of the Hemings' descendants, Eston Hemings, it's inconceivable that Jefferson, who was 65 when Eston was born, would have made a one-night stand here. I think this is a longstanding relationship. When it began and what the character of the relationship is we probably can't know easily or at all. But it was, without question, an enduring one.
- "Interview: Joseph Ellis", Jefferson's Blood, 2000, PBS-Frontline, Quote: "We don't know for sure when Jefferson's relationship with Sally Hemings started. The DNA testing that has been done was done on the Eston Hemings line. Eston was born in 1805. It does seem that Jefferson had a long-term relationship with Sally Hemings."
- John, Marshall (2004-12-07). "Ellis doesn't want to revisit his own past". Seattle Post Intelligencer. Retrieved 2008-07-08.
- Ellis, Joseph (2001-08-17). "Further Statement of Joseph J. Ellis". mountholyoke.edu. Archived from the original on 2006-07-15. Retrieved 2006-08-04.
- Creighton, Joanne (2001-08-17). "A Letter to the Mount Holyoke Community". mountholyoke.edu. Archived from the original on June 21, 2006. Retrieved 2006-08-04.
- "Trustees Name Four Faculty Members to Endowed Chairs". "Mount Holyoke College. 2005-05-20.
- "2001 Pulitzer Prize Winners". pulitzer.org. 2001. Retrieved 2006-08-04.
- "Online Catalog. Random House for High School Teachers.
- "Joseph J. Ellis". Random House: Authors.
- Book summary
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