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Background: Recurrence and distant metastasis are still the main problems affecting the long-term prognosis of nasopharyngeal carcinoma (NPC) patients, and may be related to the Ki-67 proliferation status. We therefore explored the potential correlation between Ki-67 proliferation status in NPC with the parameters derived from two imaging techniques: three-dimensional pulsed continuous arterial spin labeling (3D pCASL) and intravoxel incoherent motion (IVIM).Methods: Thirty-six patients with pathologically confirmed NPC were included, and the Ki-67 labeling index (LI) was measured by immunohistochemistry. All patients underwent plain and contrast-enhanced magnetic resonance imaging (MRI), IVIM, and 3D pCASL examination. The mean, maximum, and minimum of blood flow (BF), minimum of apparent diffusion coefficient (ADC), pure diffusion coefficient (D), pseudodiffusion coefficient (D*), and perfusion fraction (f) parameters were all measured, and Spearman's correlation analysis was performed to evaluate the relationships between these parameters and the Ki-67 LI.According to the Ki-67 values, the patients were divided into two groups: high (>50%) and low (≤50%). The rank-sum test (Mann-Whitney U test) was then used to compare the differences in quantitative parameters between the high and low Ki-67 groups.Results: Ki-67 LI was positively correlated with BF mean and BF max (r=0.415 and 0.425). D* mean and D* min did have positive correlation with Ki-67, but this was not significant (P=0.082 and 0.072). BF max was significantly different between the high and low Ki-67 groups (P=0.028).Conclusions: 3D pCASL and IVIM are noninvasive functional MR perfusion imaging techniques that can evaluate perfusion information and perfusion parameters. Our study suggests that 3D pCASL is more effective than IVIM for assessing the proliferation status of NPC, which is beneficial for evaluating the prognosis of patients. Furthermore, BF max is the best biomarker for distinguishing high from low Ki-67 levels.