Cortical and subcortical gray matter (GM) are histologically different and have different DTI values. In this study, we measured the microscopic fractional anisotropy (μFA) of cortical and subcortical GM in healthy subjects using double-diffusion encoding. We confirmed that the μFA and fractional anisotropyof subcortical GM were higher than those of cortical GM. Additionally, the μFA in the globus pallidus was high than in the striatum. Myelin was higher in subcortical GM than in cortical GM, and it was higher in globus pallidus than in the striatum; therefore, higher μFA may reflect these histological features.