Cold Case frequently features LGBTQ+ characters, often as victims of crimes motivated by prejudice. While outcomes are tragic, the show's narrative consistently condemns homophobia and transphobia, portraying LGBTQ+ individuals with dignity and empathy, and affirming the value of their lives and relationships.

Cold Case features multiple episodes centered on the murders of transsexual women. The series consistently portrays these characters with dignity and empathy, highlighting their struggles for identity and acceptance. While their stories often end tragically due to external prejudice and violence, the narrative affirms the worth of their lives and condemns the discrimination they faced.

The series often exposes crimes and injustices within institutions historically affiliated with Christianity, such as orphanages or schools, highlighting their failures, abuses, or cover-ups. While individual faith might be present, the narrative frequently critiques the problematic actions of these institutions without offering a significant counterbalancing positive portrayal of the faith itself.