PURPOSE: The purpose of this study was to describe baseline physical and laboratory characteristics of participants in the largest prospective study of transgender and gender-diverse (TGD) youth in the United States. METHODS: Participants were recruited from four clinics which specialize in the care of TGD youth before starting either GnRH analogs for pubertal suppression or gender-affirming hormone treatment. Anthropometric and laboratory measurements were abstracted from the medical chart. Baseline characteristics including height, weight, body mass index, blood pressure, and laboratory measurements were compared with those of age-matched National Health and Nutritional Examination Survey comparison group. RESULTS: Seventy-eight TGD youth with a median age of 11 years (range 8-14 years) were recruited before pubertal suppression, of whom 41 (53%) were designated male at birth, and 296 participants with a median age of 16 years (range 12-20 years) were recruited before beginning gender-affirming hormones, of whom 99 (33%) were designated male at birth. The mean high-density lipoprotein cholesterol was lower in the study participants when compared with that of National Health and Nutritional Examination Survey participants (50.6 ± 12.3 mg/dL vs. 53.3 ± 13.3 mg/dL, p = .001). Otherwise, the study cohorts were similar in terms of body mass index, proportion of overweight and obesity, blood pressure, and baseline laboratory variables. CONCLUSIONS: Before starting gender-affirming treatment, TGD youth are physiologically similar to the general population of children and adolescents in the United States, with the exception of slightly lower high-density lipoprotein cholesterol. Evaluation of this cohort over time will define the physiological effects of pubertal blockade and gender-affirming hormone treatment.