Large imaging genetic studies are becoming increasingly common in psychiatric research. In order to fully explore the collected information, analytical strategies that allow comprehensive investigations of the genetic and neural underpinnings of psychiatric disorders are needed. On the basis of our experience with the IMAGEN study, this review evaluates univariate and multivariate analytical strategies for exploring large imaging genetic datasets, with particular focus on reinforcement mechanisms in adolescents. Heritability estimates of functional and structural MRI endophenotypes are presented along with analytical strategies, ranging from those used in univariate candidate gene studies to genome-wide association studies. Finally, data reduction strategies are discussed at both the genotype level, in the form of expression SNPs and pathway analyses, and the phenotype level, as network analyses of neuroimaging data. Overall, imaging genetic studies have the potential to significantly contribute to our understanding of neurophysiological processes underlying human behavior. The analytical strategies presented here may aid in the comprehensive investigation of reinforcement and other neurobehavioral phenotypes.