OBJECTIVES: To identify and examine demographic variation in estimates of gender-diverse youth (GDY) populations from the PEDSnet learning health system network and the Youth Risk Behavior Survey (YRBS). METHODS: The PEDSnet sample included 14- to 17-years-old patients who had ≥2 encounters at a member institution before March 2022, with at least 1 encounter in the previous 18 months. The YRBS sample included pooled data from 14- to 17-year-old in-school youth from the 2017, 2019, and 2021 survey years. Adjusted logistic regression models tested for associations between demographic characteristics and gender dysphoria (GD) diagnosis (PEDSnet) or self-reported transgender identity (YRBS). RESULTS: The PEDSnet sample included 392 348 patients and the YRBS sample included 270 177 youth. A total of 3453 (0.9%) patients in PEDSnet had a GD diagnosis and 5262 (1.9%) youth in YRBS self-identified as transgender. In PEDSnet, adjusted logistic regression indicated significantly lower likelihood of GD diagnosis among patients whose electronic medical record-reported sex was male and among patients who identified as Asian, Black/African American, and Hispanic/Latino/a/x/e. In contrast, in the YRBS sample, only youth whose sex was male had a lower likelihood of transgender identity. CONCLUSIONS: GDY are underrepresented in health system data, particularly those whose electronic medical record-reported sex is male, and Asian, Black/African American, and Hispanic/Latino/a/x/e youth. Collecting more accurate gender identity information in health systems and surveys may help better understand the health-related needs and experiences of GDY and support the development of targeted interventions to promote more equitable care provision.