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The Sally Hemings controversy
For more details on this topic, see Jefferson DNA Data.
A subject of considerable controversy since Jefferson's time was whether he was the father of any of the children of his slave Sally Hemings. Hemings, the daughter of John Wayles, Jefferson's former father-in-law, was the half sister of Jefferson's deceased wife Martha Wayles Skelton Jefferson. A full account of the Hemings controversy, including discussion of DNA findings, can be found in the Sally Hemings article.

Three studies were released in the early 2000s, following the publication of the DNA evidence. A study by the Thomas Jefferson Foundation which runs Monticello states that "it is very unlikely that...any Jefferson other than Thomas Jefferson was the father of her children." A study commissioned by the Thomas Jefferson Heritage Society concludes that the Jefferson paternity thesis is not persuasive. The National Genealogical Society Quarterly then published articles reviewing the evidence from a genealogical perspective and concluding that the link between Thomas Jefferson and Sally Hemings was valid.

David N. Mayer, a member of the Scholars Commission, says in his own writings that there is "the possibility that Jefferson's brother Randolph or one of Randolph Jefferson's five sons could have fathered one or more of Sally Hemings' children." He states that "eight of these 25 Jefferson males lived within 20 miles (a half-day's ride) of Monticello—including Thomas Jefferson's younger brother, Randolph Jefferson, and Randolph's five sons, who ranged in age from about 17 to 26 at the time of Eston's birth." All of these men could have passed down the Y chromosome that links patrilineal descendants of Eston Hemings to the Jefferson family. However, only Thomas Jefferson is documented as having been at Monticello at the time Eston Hemings and all of his siblings were conceived; only Thomas Jefferson exercised ownership control over Sally Hemings and her children; and only Thomas Jefferson was described in print as the father of those children before the DNA findings.

There is less evidence to support the allegation, published by James Callender in 1802, that Jefferson and Sally Hemings conceived a son named "Tom." That son was reportedly conceived in France. Madison Hemings stated that his mother and Thomas Jefferson did conceive a child in France, but that it "lived but a short time." The descendants of Thomas Woodson continue to publish arguments that he was the reported "Tom," sent away from Monticello to avoid scandal, but there is no DNA link between that family and Jefferson.