NCIS features several recurring and episodic LGBTQ+ characters whose identities are presented incidentally and respectfully. The show generally avoids negative stereotypes or mockery, but also doesn't deeply explore or affirm LGBTQ+ experiences, resulting in a largely neutral portrayal where queer identity is present but not central.

NCIS has featured transsexual characters in multiple episodes, consistently portraying them with dignity and respect. The narrative often positions the NCIS team as allies, actively condemning prejudice and defending these characters against discrimination. This approach frames obstacles as external, affirming the worth of trans lives and resulting in a net positive portrayal.

The show features Ziva David, a highly skilled former Mossad officer, who repeatedly engages in and wins close-quarters physical combat against male adversaries using martial arts and hand-to-hand techniques.

NCIS frequently portrays Christian characters, military chaplains, and religious communities with respect, often highlighting their supportive roles and individual faith journeys. While extremist groups sometimes appropriate Christian symbols, the narrative consistently condemns their actions, distinguishing them from mainstream Christianity.

Despite dealing with terrorism plots, NCIS makes a clear narrative distinction between extremist ideologies and the vast majority of peaceful Muslims. The show often portrays Muslim characters with nuance, condemns Islamophobia, and features them as victims, heroes, or ordinary citizens.

When Jewish characters or themes appear, NCIS consistently treats them with dignity and respect. The show avoids negative stereotypes and often portrays Jewish individuals as integral, valued members of society or the military.