Prepubertal transgender, nonbinary, and gender-diverse (TGD) children (ie, those asserting gender identity, expressing gender-role behavior outside of culturally defined norms for their sex registered at birth, or both) are presenting in greater numbers to pediatric gender clinics across the United States and abroad. A large subset of TGD children experiences gender dysphoria, that is, distress that arises from the incongruence between gender identity and sex registered at birth. A lack of consensus exists regarding care for prepubertal TGD children due, in part, to a dearth of empirical research on longitudinal developmental trajectories of gender identity, role behavior, and gender dysphoria (when present). The objective of this National Institutes of Health-funded study is to provide evidence to inform clinical care for prepubertal TGD children by establishing a US longitudinal cohort (N=248) of prepubertal TGD children and their caregivers that is followed prospectively at 6-month intervals across 18 months. At each timepoint, clinical and behavioral data are collected via web-based visit from child and caregiver reporters. Latent class analysis, among other methods, is used to identify subgroups and longitudinally characterize the gender identity and gender-role behavior of TGD children. These models will define longitudinal patterns of gender identity stability and characterize the relationship between TGD classes and mental and behavioral health outcomes, including the moderating role of social gender transition (when present), on these associations. Baseline data collection (N=248) is complete, and the identification of TGD subgroups based on gender identity and expression using latent class analysis is anticipated in 2024. The completion of all 4 waves of data collection is anticipated in July 2024, coinciding with the start of a no-cost study extension period. We anticipate longitudinal analyses to be completed by winter 2024. Through a longitudinal observational design, this research involving prepubertal TGD children and their caregivers aims to provide empirical knowledge on gender development in a US sample of TGD children, their mental health symptomology and functioning over time, and how family initiated social gender transition may predict or alleviate mental health symptoms or diagnoses. The research findings have promise for clinicians and families aiming to ensure the best developmental outcome for these children as they develop into adolescents. DERR1-10.2196/55558.