Whitaker was born in the Los Angeles neighborhood of Van Nuys, the fifth of eight children of Thelma and John O. Whitaker, Sr.
Whitaker began his professional acting career at the age of three by appearing in a television commercial for a local used-car dealer. He went on to appear in advertisements for Mattel Toymakers, for such toys as Larry the Lion and Crackers the Parrot in their Animal Yackers series. In 1965, Whitaker originated the character of the young Scotty Baldwin in the soap opera General Hospital. In 1966, he acted in a major feature film, The Russians Are Coming, the Russians Are Coming, which also starred Brian Keith. After Keith was cast as the lead in the television series Family Affair, he recommended Whitaker to play the part of his on-screen nephew.
Family Affair aired from 1966 to 1971. It co-starred Whitaker playing the role of an orphaned boy named Jody Davis, living in a high-rise apartment in New York City with his twin sister Buffy (Anissa Jones) and older sister Cissy (Kathy Garver), his bachelor uncle Bill Davis (Brian Keith), and Bill's gentleman's gentleman, Mr. French (Sebastian Cabot). Jody and Buffy were originally supposed to be different ages, but the show's producers thought Whitaker and Jones looked so cute together that they changed them to be twins. While a regular on the show, Whitaker also starred in the Hallmark Hall of Fame production The Littlest Angel alongside Fred Gwynne and Tony Randall, and an episode of the long-running Western The Virginian in 1969.

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