Abstract Transgender people experience harassment, denial of services, and physical assault during healthcare visits. Electronic health record (EHR) structure and language can exacerbate the harm they experience by using transphobic terminology, emphasizing binary genders, and pathologizing transness. Here, we investigate the ways in which SNOMED CT and ICD-10-CM record gender-related terminology and explore their shortcomings as they contribute to this EHR-mediated violence. We discuss how this “standardized” gender-related medical terminology pathologizes transness, fails to accommodate nonbinary patients, and uses derogatory and outmoded language. We conclude that there is no easy fix to the transphobia beleaguering healthcare, provide options to reduce harm to patients, and ultimately call for a critical examination of medicine’s role in transphobia. We aim to demonstrate the ways in which the [mis]use and [mis]understanding of gender-specific terminology in healthcare settings has harmed and continues to harm trans people by grounding our discussion in our personal experiences.