Background Reduced amygdala volume has been implicated in the development of severe and persistent aggression and the development of psychopathic personality. With longitudinal data, the current study examined whether male subjects with lower amygdala volume have a history of aggression and psychopathic features dating back to childhood and are at increased risk for engaging in future aggression/violence. Methods Participants were selected from a longitudinal study of 503 male subjects initially recruited when they were in the first grade in 1986–1987. At age 26, a subsample of 56 men with varying histories of violence was recruited for a neuroimaging substudy. Automated segmentation was used to index individual differences in amygdala volume. Analyses examined the association between amygdala volume and levels of aggression and psychopathic features of participants measured in childhood and adolescence. Analyses also examined whether amygdala volume was associated with violence and psychopathic traits assessed at a 3-year follow-up. Results Men with lower amygdala volume exhibited higher levels of aggression and psychopathic features from childhood to adulthood. Lower amygdala volume was also associated with aggression, violence, and psychopathic traits at a 3-year follow-up, even after controlling for earlier levels of these features. All effects remained after accounting for several potential confounds. Conclusions This represents the first prospective study to demonstrate that men with lower amygdala volume have a longstanding history of aggression and psychopathic features and are at increased risk for committing future violence. Studies should further examine whether specific amygdala abnormalities might be a useful biomarker for severe and persistent aggression.