A variety of school-based, universal preventive interventions have been developed to address behavioral and mental health problems. Unfortunately, few have been evaluated within the context of randomized controlled trials with long-term follow-up. Even fewer still have examined the potential genetic factors that may drive differential impact of the intervention. In the present analysis, we examine the extent to which the longitudinal effects of two elementary school-based interventions were moderated by the brain-derived neurotrophic factor (BDNF) gene, which has been linked with aggression and impulsive behaviors. The sample included 678 urban, primarily African American children who were randomly assigned along with their teachers to one of three first grade classroom conditions: classroom-centered (CC) intervention, Family School Partnership (FSP), or a control condition. The teacher ratings of the youth's aggressive and impulsive behavior were obtained at baseline and in grades 6-12. Single-nucleotide polymorphisms (SNPs) from the BDNF gene were extracted from the genome-wide data. Longitudinal latent trait-state-error models indicated a significant interaction between a particular profile of the BDNF SNP cluster (46 % of sample) and CC intervention on impulsivity (β = -.27, p < .05). A similar interaction was observed for the BDNF SNP cluster and the CC intervention on aggression (β = -.14, p < .05). The results suggest that the impacts of preventive interventions in early elementary school on late adolescent outcomes of impulsivity and aggression can be potentially modified by genetic factors, such as BDNF. However, replication of these results is necessary before firm conclusions can be drawn.