Gates's family is descended in part from the Yoruba people of west Africa. He also has some European ancestry, and is connected to the distinctive multiracial West Virginia community of the Chestnut Ridge people. He is also of part Irish descent.
Henry Louis Gates Jr. was born in Keyser, West Virginia to Henry Louis Gates Sr. (c.1913–2010) and his wife Pauline Augusta (Coleman) Gates (1916–1987). He grew up in neighboring Piedmont. His father worked in a paper mill and moonlighted as a janitor, while his mother cleaned houses.