DNA testing finally confirmed this to be fact in the late 1990's. And it remains the subject of much interest to this day.
Two local descendants of Thomas Jefferson and Sally Hemmings, his slave mistress, tell a captivating the story of the children he fathered with her.
Their stories take us to a minister from North Wales and a man from Norristown, Pennsylvania, and they reflect a complicated history of tangled blood lines.
"We actually found out that I was a direct descendant through a straight male line from Thomas Jefferson through one of his servants, Sally Hemmings.
John Weeks Jefferson spoke publicly for the first time about his ancestry. He says his family has always known about their connection to Thomas Jefferson, but he said, "They thought, as well as I did that I was a distant relative or cousin."
It was a remarkable event when the testing of his DNA concluded that John was Thomas Jefferson's third generation grandson, and Eston Hemmings, Jefferson's youngest son with his slave, Sally, was his great, great-grandfather.
When asked if he thought it was a taboo subject for his family, Jefferson said, "I think so, maybe they were embarrassed if it ever should come out."
Historians say the relationship between Thomas Jefferson and Sally Hemmings, seen in some artists' renderings, continued for more than thirty-five years at Monticello, his former plantation, in Charlottesville, Virginia.
"Anytime you live a lie, not in the sense of your race, but in a sense of who you are related to, that's a big deal to leave family behind," says Historian Annette Gordon-Reed.
Annette Gordon-Reed is a leading historian of slavery, who won a 2009 Pulitzer prize in history for her book, "The Hemmings of Monticello, An American Family".
She says after the Civil War, race was determined by the "one drop rule".
"If you had one drop of black blood, you were considered a black person, no matter how white you looked, no matter what, that was the rule," said Gordon-Reed.
Gordon-Reed says light-skinned former slaves, like John's third generation grandmother, Sally Hemmings, often "passed" as white, denying their heritage.
"His ancestors at some point decided that they wanted to live as white people, and to do so, they had to reject Sally Hemmings," explains Gordon-Reed.
Jefferson was asked if it ever crossed his mind that with the knowledge of his ancestry, that he was, by American standards, black.
"I wasn't embarrassed like they probably would have been," said Jefferson. "I was proud of my American heritage."
Historians say Jefferson's and Hemmings' only child who lived as black was his son, Madison, the 6th generation grandfather of the Reverend Doug Banks, of North Wales.
"Thomas Jefferson is my great, great, great, great, great, great, great grandfather," said Rev. W. Douglas Banks.
Reverend Banks, with his son, DJ, has known his ancestry as long as he can remember. But as a black man, he's ambivalent about it.
Thomas Jefferson is kind of like a part of my human history. He doesn't define it," said Rev. Banks. "I've always seen myself as a descendant of slaves that Thomas Jefferson owned.
"This is the stuff of human life, and you have to be honest about it," says Gordon-Reed.
There are many more stories like that of Thomas Jefferson and Sally Hemmings.
John Jefferson fully embraces his black heritage. For Reverend Banks, it still represents a tragic hypocrisy in the life of a brilliant man, who denounced slavery, but as Annette Gordon-Reed put it, had a set of intellectual beliefs he couldn't live up to emotionally.
It was Thomas Jefferson who said, "You should follow the truth to wherever it leads."