Several large imaging-genetics consortia aim to identify genetic variants influencing subcortical brain volumes. We investigated the extent to which genetic variation accounts for the variation in subcortical volumes, including thalamus, amygdala, putamen, caudate nucleus, globus pallidus and nucleus accumbens and obtained the stability of these brain volumes over a five-year period. The heritability estimates for all subcortical regions were high, with the highest heritability estimates observed for the thalamus (80) and caudate nucleus (88) and lowest for the left nucleus accumbens (44). Five-year stability was substantial and higher for larger [e.g., thalamus (88), putamen (86), caudate nucleus (87)] compared to smaller [nucleus accumbens (45)] subcortical structures. These results provide additional evidence that subcortical structures are promising starting points for identifying genetic variants that influence brain structure. © 2013 Elsevier Inc.