Because Haley discussed his massive research and claimed that the family accounts in Virginia and North Carolina were based on verifiable documented facts, critics were disconcerted when checking revealed that not to be the case. They could have accepted a novel and judged it on its own terms, but Haley claimed it to be "true". Although Haley acknowledged the novel was primarily a work of fiction (he described it as "faction"), he claimed that his ancestor was Kunta Kinte, an African taken from the village of Juffure in what is now the Gambia. He said that Kunta Kinte was sold into slavery where he was given the name Toby. While held by John Waller, Kinte had a daughter named Kizzy, who was Haley's great-great-great grandmother. Haley said that he had identified the slave ship that transported Kunta Kinte from Africa to North America in 1767.
Haley also suggested that his portrayal of life and figures among the slaves and masters in Virginia and North Carolina were based on facts which he had confirmed through historical documents. In the concluding chapter of Roots Alex Haley wrote:
|“||To the best of my knowledge and of my effort, every lineage statement within Roots is from either my African or American families' carefully preserved oral history, much of which I have been able conventionally to corroborate with documents. Those documents, along with the myriad textural details of what were contemporary indigenous lifestyles, cultural history, and such that give Roots flesh have come from years of intensive research in fifty-odd libraries, archives, and other repositories on three continents.||”|
Haley said that most of the dialogue and necessary incidents were fictional, based on what he knew took place and what the research led him to feel took place.
Historians and genealogists have said that he did not rely on facts as closely as he represented. For example, researchers have cast doubts on whether Haley tracked his ancestry to a specific village and individual, or was being told what he wanted to hear by the people who lived there. Donald R. Wright, an Africanist historian, and Gary B. and Elizabeth Shown Mills, a historian and a genealogist, respectively, who specialize in African-American and southern history, separately revisited parts of Haley's research. They concluded he was unlikely to have been able to make all the stated connections. The Millses found that historical documents strongly contradicted his accounts allegedly based on fact of family history in the colonies.
Professor Wright focused on Haley's identification and portrayal of alleged African ancestors. He noted the unreliability of twentieth-century griots and village elders for historical accounts of the 1700s, and significant inaccuracies in the portrayal of Juffure as a pastoral village.
Several years later, the Millses published an article that focused upon Haley's identification and portrayal of four generations of slave forebears and masters in Virginia and North Carolina. Their reporting concluded: "Those same plantation records, wills, and censuses cited by Mr. Haley not only fail to document his story, but they contradict each and every pre-Civil War statement of Afro-American lineage in 'Roots'."  They fault Haley for failing to reconcile his family stories by giving precedence to the facts found in documents and other evidence, rather than oral histories, but presenting his work as factually based. Among other differences, they found several records of a slave named Toby being held by the Waller family five years before his arrival by slave ship in Virginia, as told by Haley. They concluded the many contradictions weakened the author's assertion that "By 1967, I felt I had the seven generations of the U.S. side documented."
The Millses also make "the obvious point" that "Chicken George's presence in England in the 1850s, where slavery was illegal, would have won him automatic freedom under both English and American law". The English decision in Somerset's case of 1772 was widely discussed in America prior to the Civil War.
Haley criticized his detractors' reliance upon written records in their evaluation of his work, contending that such records were "sporadic" and frequently inaccurate with regard to such data as slave births and ownership transactions. Haley asserted that for African-American genealogy, "well-kept oral history is without question the best source."
Concerns were raised about the trustworthiness of Kebba Fofana from the Gambia, whom Haley had cited as a significant source. He said Fofana was a griot in Juffure, who, during Haley's visit, confirmed the tale of the disappearance of Kunta Kinte. The separate investigations by Mark Ottaway of The Sunday Times and Professor Wright found that Fofana was not a genuine griot, and that he was aware of Haley's pending visit. He may have been coached to relate a story matching Haley's chronicle. In subsequent re-tellings, details of Fofana's story failed to match that first account. Haley did not respond directly to the work of either Wright or Ottaway, but said that the latter's article was "unwarranted, unfair and unjust", and added that he had no reason to think Fofana unreliable.
Harvard University professor Dr. Henry Louis Gates, Jr. was a personal friend of Haley, but years after his death Gates acknowledged doubts about the author's claims. He said,
"Most of us feel it's highly unlikely that Alex actually found the village whence his ancestors sprang. Roots is a work of the imagination rather than strict historical scholarship. It was an important event because it captured everyone's imagination."
Gates later was the host of African American Lives, a TV series that relied on research by historians and genealogists, but also on DNA testing, to reveal to prominent American figures facts of their family histories.