The HEALthy Brain and Child Development (HBCD) Study, a multi-site prospective longitudinal cohort study, will examine human brain, cognitive, behavioral, social and emotional development beginning prenatally and planned through early childhood. Many prenatal and early childhood exposures impact both later physical health and development. Moreover, early deficits in physical health, such as growth and vision, are associated with differences in brain development, language and cognitive functioning. For these reasons, the HBCD Study includes measures of early childhood physical health, many of which have clinical relevance, and are applicable for use as both predictors and outcomes. Study measures assess a broad range of physical health domains and include both objective measurement of child growth and health and subjective caregiver report of behaviors and attitudes about constructs known to influence growth and physical development. Lastly, we obtain caregiver report of the child’s routine medical care as well as acute and chronic medical issues. We anticipate that these data will contextualize the impact of child physical growth and health on child brain development and function. In this report we present the rationale for each domain and an overview of the physical health measures included in the current HBCD Study protocol.