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 consistently portrays Christianity, primarily through Turk, as a source of moral guidance, strength, and community. While comedic elements exist, the narrative respects the faith and its positive impact on characters, even when challenged by cynical characters.

Judaism is depicted as a respected cultural and familial background for Elliot, occasionally referenced for lighthearted humor or to explore her identity. The portrayal is generally respectful and does not attach negative weight to the faith itself.