TOF-MRA at 7T ultra-high field has been proven to have advantages in imaging the perforating arteries originating from the middle cerebral artery. In this study, a novel method of VOI-based micro-vessel density measurement was developed to quantitatively assess the blood flow in subcortical nuclei. Using this technique, the vascular density (VD) of specific basal ganglia sub-regions can be evaluated. Preliminary results showed that VD values of specific nuclei were different among Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalophy (CADASIL) patients, stroke patients, and healthy volunteers. VOI-based micro-vessel density measurement may be useful in differentiating the etiology of cerebral small vessel diseases.