Adolescence is characterized by dynamic changes in structural brain maturation. At the same time, adolescence is a critical time for the development of affective and anxiety-related disorders. Individual differences in typically developing children and adolescents may prove more valuable for identifying which brain regions correspond with internalizing behavior problems (i.e., anxious/depressive, withdrawal and somatic symptoms) on a continuous scale compared to clinical studies. Participants were 179 (92 males, 87 females) typically developing children and adolescents between ages 8 and 17. Hippocampal and amygdala volumes were measured automatically with FreeSurfer. Internalizing behavior was assessed with the Child Behavior Checklist (CBCL) completed by the parent, and associated with hippocampal and amygdala volumes. Hippocampal volume was inversely related with the total internalizing problems scale of the CBCL, irrespective of gender, age, or informant (mother or father). The effects were most prominent for the withdrawal and anxiety/depression subscales and the left hippocampus: more withdrawal and anxiety/depression was related to smaller left hippocampal volume. No associations were found between internalizing behavior and amygdala volume. This study shows that typically developing children and adolescents with high internalizing behavior share some of the neuroanatomical features of adult depression and anxiety-related disorders.