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Widespread use of antiretroviral therapy (ART) in human immunodeficiency virus (HIV) patients has led to improved longevity with the attendant increase in noncommunicable disease prevalence including chronic kidney disease (CKD). This study documents the prevalence of CKD in a large HIV population in Southern Nigeria.This is a single center, 15-year analysis in ART-naïve patients. CKD was defined as the occurrence of estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 on 2 consecutive occasions 3 to 12 months apart using the chronic kidney disease epidemiology collaboration (CKD-EPI) equation. The Cochran-Armitage and Cuzick tests were employed to assess for trend across the years for CKD prevalence and CD4 count, respectively. Multivariable logistic regression models were used to identify independent associations with CKD.In all, 1317 patients (62.2% females) with mean age of 34.5 years and median CD4 count of 194 cells/μL were included. CKD prevalence was 13.4% (95%CI 11.6%–15.4%) using the CKD-EPI equation (without the race factor). Multivariable analysis identified increasing age and CD4 count <200 cells/μL as being independently associated with CKD occurrence.This study reports a high prevalence of CKD in ART-naïve HIV-infected patients. Measures to improve diagnosis of kidney disease and ensure early initiation of treatment should be integrated in HIV treatment programmes in this setting.