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Introduction South Africa has the highest prevalence of HIV in the world. The epidemiology of kidney disease among people with HIV infections is well-described in the United States. However, there are limited data coming from South Africa, particularly that involve kidney biopsies. The purpose of this study was to determine what, if any, patient factors are predictive of HIV-associated nephropathy (HIVAN) on kidney biopsy in a South African kidney biopsy cohort. Methods This study prospectively collected data of all patients infected with HIV referred to the Groote Schuur Hospital (GSH) renal unit for a kidney biopsy from 2002 to 2018. Results There were 419 patients included in the study. Mean age was 36.5 years (SD, 9.4); 219 (52.3%) were women; and all were black. Seventy-nine patients (18.9%) were on dialysis at the time of biopsy; the mean estimated glomerular filtration rate among the remainder was 41.4 ml/min per 1.73 m2 (SD, 39.2). Only 163 patients (47.1%) were known to be taking antiretroviral therapy (ART) at the time of biopsy. There were 246 (58.7%) cases of HIVAN detected, and they were comparable on age, sex, kidney function, and kidney size to those with kidney disease of other causes but were less likely to be taking ART (P < 0.001). Biopsy confirmed HIVAN was associated with mortality (adjusted hazard ratio, 1.77; 95% confidence interval [CI]: 1.07–2.91; P = 0.025), and the use of ART at biopsy was protective (adjusted hazard ratio, 0.52; 95% CI, 0.32–0.84, P = 0.008). The proportion of HIVAN on biopsy decreased and the proportion taking ART increased from 2002 to 2018 (P for trend for both < 0.001). Conclusion In summary, HIVAN was the most common etiology of kidney disease in this biopsy cohort from South Africa; however, the proportion with biopsy-proven HIVAN declined over time, perhaps in the setting of greater ART availability., Graphical abstract