A significant part of Ziva's time on the show focuses on her relationship with her home country and, more specifically, her relationship with her father, Eli David (Michael Nouri), the director of Israel's intelligence agency, Mossad. Ziva's childhood is repeatedly alluded to as having been difficult, and her estrangement from her father is a source of deep pain. Her killing of Ari only served further to divide the strained relationship between father and daughter.

In Season 6 and Season 7, Ziva is kidnapped by Somali terrorists and is tortured in a training camp. Her three closest friends — Gibbs, Tony, and McGee — eventually rescue her at NCIS, but her father is primarily seen as indifferent to her struggles and sees her divided loyalty between NCIS and Mossad as a liability. Ziva remarks that her father treated her "like more of a Mossad officer than a daughter." In the Season 10 episode "Shabbat Shalom," Eli David is killed in a drive-by shooting that also claims the life of NCIS Director Leon Vance's wife, Jackie.