Objective: To investigate alterations of blood perfusion in subcortical regions in patients with Parkinson’s disease (PD) by three dimentional arterial spin labeling (ASL) magnetic resonance imaging (MRI).Methods: Thirty patients with PD and 40 control subjects were recruited from the inpatient and outpatient of the Department of Neurology of Northern Jiangsu People’s Hospital during October 2014 to October 2016, and routine brain MRI and 3D pseudo-continuous pulse ASL were performed on all the subjects. The cerebral blood flow (CBF) maps derived from 3D ASL were coregistered to the Montreal Neurological Institute brain space. The stereo-templates of bilateral caudate nucleus, putamen nucleus, globus pallidum and thalamus from Anatomical Automatic Labeling were used as region of interest (ROI) to exstract absolute CBF values in these subcortical regions, respectively. The CBF ratio (rCBF) values represented by individual whole brain CBF divided by each of the regional CBF were also calculated in consideration of the difference between individual whole brain CBF. The CBF and rCBF values were compared respectively between groups by one-way analysis of variance.Results: The subcortical CBF values (ml•100 g-1•min-1) for each ROI in PD (caudate nucleus (left: 35.32±6.47, right: 36.17±7.07), globus pallidum (left: 40.42±5.83, right: 40.18±5.70), putamen nucleus (left: 41.97±6.12, right: 42.91±6.43) and thalamus (left: 46.58±7.71, right: 49.11±7.10)) were significantly lower than that in the control group (caudate nucleus (left: 41.38±7.05, right: 41.63±6.85), globus pallidum (left: 45.65±8.35, right: 45.53±8.94), putamen nucleus (left: 48.49±8.78, right: 48.99±8.88) and thalamus (left: 54.32±11.94, right: 56.21±11.98), F=13.58, 10.56, 12.11, 10.06, 8.59, 8.23, 9.57, 8.30, P=0.000, 0.002, 0.005, 0.005, 0.001, 0.002, 0.003, 0.005, respectively). The whole brain mean CBF values of each subject were also extracted and compared bewteen groups, and mean CBF values (ml•100 g-1•min-1) in PD patients (42.14±9.61) decreased significantly than those in the control group (51.59±9.67, F=16.42, P<0.01), and there was a 18.31% decrement in whole brain mean CBF in the patient group. However, rCBF values for almost all subcortical ROIs of the patients significantly increased when compared with the control group.Conclusions: The decreased absolute cerebral blood perfusion involved not only subcortical regions, but also the whole brain level in the course of PD. The CBF metabolism in patients with PD may have been redistributed, with relative hyperperfusion in the subcortical brain regions contrast to the whole brain perfusion level of patients themselves. Copyright © 2019 by the Chinese Medical Association.