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ObjectivesStudies have recently shown an alteration of the structural connectivity and a dysfunctional glymphatic system in patients with chronic kidney disease (CKD). In this study, we aimed to investigate the effects of the structural connectivity and glymphatic system on the cognitive function of patients with CKD.MethodsWe prospectively enrolled patients with CKD and healthy controls. The CKD group was divided into two regarding their cognitive function. All patients received brain magnetic resonance imaging, including diffusion tensor imaging (DTI). We calculated the measures of structural connectivity and diffusion tensor image analysis along the perivascular space (DTI-ALPS) index, a neuroimaging marker of the glymphatic system function, and compared the indices between groups.ResultsThe mean clustering coefficient, local efficiency, and small-worldness index in patients with CKD were lower than those in healthy controls (0.125 ± 0.056 vs. 0.167 ± 0.082, p = 0.008; 1.191 ± 0.183 vs. 1.525 ± 0.651, p = 0.002; 0.090 ± 0.043 vs. 0.143 ± 0.102, p = 0.003; respectively). The DTI-ALPS index was lower in patients with CKD than in healthy controls (1.436 vs. 1.632, p