Jonathan Howsmon Davis was born in Bakersfield, California, on January 18, 1971, the son of Holly Marie (née Smith; born May 6, 1949) Chavez and Ricky Duane "Rick" Davis (born December 14, 1948). His parents married on February 27, 1970. He is of English, German, Scottish, and Welsh descent. He has a sister, Alyssa Marie Davis (born February 8, 1974), a half-brother, Mark Chavez (lead singer of Adema; born November 15, 1978), and a half-sister, Amanda Chavez (born July 31, 1981), by his mother. His father was a keyboardist for Buck Owens and Frank Zappa, while his mother was a professional actress and dancer. His parents divorced when he was three years old and he was raised by his father and former stepmother in Bakersfield.
Davis suffered severe bouts of asthma as a child, and survived a near-fatal asthma attack when he was five years old. He also spoke of having a horrible relationship with his former stepmother. He said she used to harass and torture him; she gave him tea mixed with Thai hot oil and jalapeño juice to drink when he was sick, locked him in cabinets, and put cigarette burns on his arms. Though she was later divorced by Davis' father, the Korn song "Kill You" was nonetheless written about her. Davis has said that his earliest musical inspiration as a child was the Andrew Lloyd Webber musical Jesus Christ Superstar, and his favorite musical group was Duran Duran. He graduated from Highland High School in 1989, and worked at Toys R Us shortly after. He also attended the San Francisco School of Mortuary Science for a period of time. He was persistently harassed in Highland High School for wearing eyeliner, long clothes, and listening to new wave music. He was constantly called homophobic names,  which later inspired the Korn song "Faget". Davis' "HIV" tattoo on his upper left arm was also inspired by his experience of being bullied. He says even teachers were mean to him and sent him to the counselor for wearing eyeliner.