Whole-genome sequencing (WGS) has advanced to a point where it is beginning to be integrated into pediatric practice. With little consensus on how to maximize the benefits of WGS for children, there is a growing need for focused efforts that connect researchers, clinicians, and families to chart a path forward. To illustrate relevant concerns, two contrasting applications of pediatric WGS are explored: clinical use with children who have undiagnosed conditions, and population-based screening. Specific challenges for health care services, policy development, and the well-being of children are discussed in light of current research. In the interest of ensuring evidence-based pediatric WGS, strategies are identified for advancing our understanding of what it means for children to grow up with WGS results guiding their health care.