Adolescence is a key period for the development of brain circuits underlying affective and behavioral regulation. It remains unclear, however, whether and how adolescent brain structure influences day-to-day affective behavior. Because of significant changes in the nature of family relations that also typically occur during adolescence, parent-child interactions provide a meaningful context where affective behavior and its regulation may be assessed. In a sample of 137 early adolescents, we investigated the relationship between aspects of the adolescents' brain structure and their affective behavior as assessed during observation of parent-child interactions. We found a significant positive association between volume of the amygdala and the duration of adolescent aggressive behavior during these interactions. We also found male-specific associations between the volume of prefrontal structures and affective behavior, with decreased leftward anterior paralimbic cortex volume asymmetry associated with increased duration of aggressive behavior, and decreased leftward orbitofrontal cortex volume asymmetry associated with increased reciprocity of dysphoric behavior. These findings suggest that adolescent brain structure is associated with affective behavior and its regulation in the context of family interactions, and that there may be gender differences in the neural mechanisms underlying affective and behavioral regulation during early adolescence. Particularly as adolescence marks a period of rapid brain maturation, our findings have implications for mental health outcomes that may be revealed later along the developmental trajectory.