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Background: Multicystic dysplastic kidney (MCDK) disease and unilateral renal agenesis (URA) are well-known causes of a solitary functioning kidney (SFK) and are associated with long-term kidney injury. The aims of this study were to characterize the natural history of SFK at our center, define the risk factors associated with chronic kidney injury, and identify distinguishing features between URA and MCDK that predict outcome. Methods: This was a retrospective cohort study of 230 SFK patients. We compared MCDK (n=160) and URA (n=70) according to clinical features at diagnosis and kidney outcomes over follow-up. Univariate and multivariate binary regression analysis was used to determine independent risk factors for chronic kidney injury, defined as the composite outcome of hypertension, proteinuria, or chronic kidney disease (eGFR <60 mL/min/1.73m2). Results: URA had a higher prevalence of comorbid genetic syndromes (15 vs. 6%, p=0.04), non-renal anomalies (39 vs. 11%, p<0.001), and congenital anomalies of the kidney and urinary tract (CAKUT) (51 vs. 26%, p<0.001) than MCDK. Over follow-up, URA experienced more hypertension (19 vs. 3%, p=0.002), proteinuria (12 vs. 3%, p=0.03), and the composite outcome (19 vs. 6%, p=0.003) than MCDK. Independent risk factors for chronic kidney injury included CAKUT (OR 5.01, p=0.002) and URA (OR 2.71, p=0.04). Conclusions: In our population, URA was more likely to have associated syndromes or anomalies, and to have worse outcomes over time than MCDK. URA diagnosis was an independent risk factor for chronic kidney injury. Our results will be used to develop a standardized clinical pathway for SFK management. [ABSTRACT FROM AUTHOR]