BACKGROUND AND PURPOSE: The pathogenesis of neurovascular diseases and various types of dementia is tightly connected to cerebral circulation. An area that requires further exploration is the system of deep cerebral perforating arteries-arteries branching directly from high-pressure intracranial arteries, supplying vital neural structures such as the internal capsule, and characterized by a diameter of well below 1 mm, which makes them difficult to visualize with standard radiological examinations. This study aimed to analyze the morphology of the perforator origins, which constitute connection points between high-pressure intracranial arteries and microcirculation. METHODS: Twenty-three human basal ganglia specimens with the middle cerebral artery (MCA, including 172 perforating arteries) and ten brainstem specimens with the basilar artery (BA, including 162 perforating arteries) were prepared and scanned using microcomputed tomography. The geometry and structure of the perforating arteries were analyzed using radiological images and additional histological studies. RESULTS: The ostia of the perforating arteries were ellipsoidal in shape with median stenosis severity of 23% and 20% for MCA and BA perforators, respectively. The local narrowing structure was typical of neointimal hyperplasia. Statistical analysis revealed that the severity of stenosis may be related to age and cardiovascular health. CONCLUSION: Origins of the deep cerebral perforators are locally narrowed by neointimal hyperplasia, which may be a protective mechanism to adjust high blood pressure to the microcirculation. The narrowings may lead to chronic hypoperfusion and play a role in the pathophysiology of cerebral small vessel disease.