Scrubs, while a comedy that sometimes uses initial ignorance for humor, ultimately portrays LGBTQ+ characters and themes with a net positive impact. The show often resolves problematic initial reactions by promoting understanding, empathy, and acceptance, particularly evident in its treatment of a transgender patient and a gay couple.

Scrubs features a trans woman character, Julie, in a single episode. Her identity is revealed as a plot point, handled with some initial surprise from other characters but without overt malice or sustained ridicule. The portrayal is incidental, neither strongly affirming nor denigrating, as her character's depth and agency regarding her identity are limited.

The show frequently portrays Christian characters, particularly Carla, whose faith is a consistent source of moral guidance, strength, and community. While other characters may question or challenge religious beliefs, the narrative often frames these challenges as personal struggles or cynicism, rather than condemning Christianity itself. The show explores the virtues and comfort faith can provide, positioning the audience to understand and often sympathize with religious viewpoints.

Jewish characters, such as Elliot and Dr. Kelso, are depicted respectfully, often as culturally Jewish rather than strictly observant. Their background is treated with nuance, and the show avoids negative stereotypes, integrating their heritage into their character development without making it problematic.