Nikos was the first-born in the family, and was followed by Anastasia, Eleni and Yiorgos, who died in infancy.

Their father, Michalis Kazantzakis (1856-1932), was a merchant and landowner who hailed from the village of Varvari, since re-named Myrtia. As a "ferocious and forbidding man", he was strict, authoritarian figure dedicated to an uncompromising code of ethics, who expected his son to honour his family traditions and Cretan descent. He rarely praised Nikos for his achievements, still less showed him any tenderness.

The counterpoint to paternal severity was maternal affection; Kazantzakis describes his mother as a "saintly woman". Named Maria Christodoulaki (1862-1932), she was originally from the village of Assyroti in the district of Mylopotamos in Rethymnon prefecture.