Baigent was born on 27 February 1948 in Nelson, New Zealand and spent his childhood in the nearby communities of Motueka and Wakefield. His father was a devout Catholic, and he was tutored in Catholic theology from the age of five. After his father left the family when Baigent was eight years old, he went to live with his maternal grandfather, Lewis Baigent and took his surname. His great-grandfather, Henry Baigent served as a Nelson city mayor and had founded a forestry firm, H. Baigent and Sons.