Ally McBeal featured several LGBTQ+ characters and storylines throughout its run, which was notable for network television in the late 1990s and early 2000s. The show explored themes of sexuality, gender identity, and same-sex relationships, often portraying these characters with dignity and addressing the societal and legal challenges they faced with empathy. The overall impact was positive, contributing to early mainstream visibility and discussion of LGBTQ+ issues.

The series features Cynthia, a pre-operative transsexual woman, portrayed with dignity and intelligence. Her storyline addresses discrimination as an external challenge, with the narrative supporting her fight for rights. A significant plot point involves John Cage developing genuine romantic feelings for her, affirming her worth and challenging societal norms. The overall portrayal is empathetic and validating.

The show consistently portrays non-traditional family structures, fluid gender roles, and a normalization of divorce, casual relationships, and chosen family over biological family, without endorsing traditional ideals.