Background: The early identification of children who have experienced adversity is critical for the timely delivery of interventions to improve coping and reduce negative consequences. Self-report is the usual practice for identifying children with exposure to adversity. However, physiological characteristics that signal the presence of disease or other exposures may provide a more objective identification strategy. This protocol describes a case–control study that assesses whether exposure to adversity is more common in children with tooth enamel anomalies compared to children without such anomalies. Methods: For 150 mother–child pairs from a pediatric dental clinic in Toronto, Canada, maternal interviews will assess the child’s adverse and resilience-building experiences. Per child, one (exfoliated or extracted) tooth will be assessed for suspected enamel anomalies. If anomalies are present, the child is a case, and if absent, the child is a control. Tooth assessment modalities will include usual practice for dental exams (visual assessment) and modalities with greater sensitivity to identify anomalies. Conclusion: If structural changes in children’s teeth are associated with exposure to adversity, routine dental exams could provide an opportunity to screen children for experiences of adversity. Affected children could be referred for follow-up.