BackgroundPatients with chronic hepatitis C virus (HCV) infections differ in their risk for metabolic disorders and chronic kidney disease (CKD). The aim of this study was to investigate the effect of metabolic disorders induced by genetic factors on CKD in HCV-infected patients.MethodsPatients with chronic non-genotype 3 HCV infection with or without CKD were examined.PNPLA3andTM6SF2variants were determined using high-throughput sequencing. The relationships of variants and different combinations with metabolic disorders were analyzed in CKD patients. Univariate and multivariate analyses were used to identify factors associated with CKD.ResultsThere were 1022 patients with chronic HCV infection, 226 with CKD and 796 without CKD. The CKD group had more severe metabolic disorders, and also had higher prevalences of liver steatosis, thePNPLA3rs738409 non-CC genotype, and theTM6SF2rs58542926 CC genotype (allP< 0.05). Relative to patients with thePNPLA3rs738409 CC genotype, patients with the non-CC genotype had a significantly decreased eGFR and a greater prevalence of advanced CKD (CKD G4-5). Patients with theTM6SF2rs58542926 CC genotype had a lower eGFR and a higher prevalence of CKD G4-5 than those with the non-CC genotype. Multivariable analysis indicated that multiple metabolic abnormalities, including liver steatosis and thePNPLA3rs738409 C > G variant, increased the risk of CKD, but theTM6SF2rs58542926 C > T variant decreased the risk of CKD.ConclusionSpecificPNPLA3rs738409 andTM6SF2rs58542926 variants are independent risk factors for CKD in patients with chronic HCV infections and are associated with the severity of renal injury.