ObjectiveThis study aimed to investigate the differences in brain morphology according to handedness.Materials and MethodsForty‐two healthy subjects were enrolled (21 right‐handers and 21 nonright‐handers). The two groups were classified according to the Edinburgh Handedness Inventory. Measures of cortical morphology, such as thickness, surface area, volume, and curvature, and the volumes of subcortical structures, such as the amygdala, caudate, hippocampus, globus pallidus, putamen, and thalamus, were compared between the groups according to handedness using whole‐brain 3D T1‐weighted MRI. In addition, we investigated the white matter differences between the groups using diffusion tensor imaging. Moreover, we quantified correlations between the handedness scales of the Edinburgh Handedness Inventory and each measure of different brain morphologies.ResultsThe volumes of the right putamen and left globus pallidus in nonright‐handed participants were significantly larger than those who were right‐handed (0.3559 vs. 0.3155%, p = .0028; 0.1101 vs. 0.0975%, p = .0025; respectively). Moreover, the volumes of the right putamen and left globus pallidus were negatively correlated with the handedness scales of the Edinburgh Handedness Inventory (r = −.392, p = .0101; r = −.361, p = .0189; respectively). However, the cortex morphology and the other subcortical volumes were not significantly different between the two groups. In addition, we did not find any white matter differences between the groups.ConclusionsWe demonstrated that there were significant differences in brain morphology between right‐handers and nonright‐handers, especially in the basal ganglia, which could produce differences in motor control according to handedness.