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Background: Small kidneys due to renal hypodysplasia (RHD) result from a decrease in nephron number. The objectives of this study were to identify clinical variables that determine long-term renal outcome in children with RHD and to define the role of kidney size as a predictor of developing end-stage renal disease (ESRD). Methods: This was a single-center retrospective cohort analysis. The primary outcome was development of ESRD. We identified 202 RHD cases, with 25 (12 %) reaching ESRD at mean age of 8.9 (±6.6) years. Results: Children with RHD with a known genetic syndrome had the smallest kidneys while those with posterior urethral valves (PUV) had the largest kidneys at diagnosis. Cases with bilateral RHD were most likely to develop ESRD. Younger gestational age (OR 0.8, CI 0.69-0.99, p = 0.05), smaller kidney size at diagnosis (OR 0.13, CI 0.03-0.47, p = 0.002), lower best-estimated glomerular filtration rate (eGFR) (OR 0.74, CI 0.58-0.93, p = 0.01), proteinuria (OR 1.03, CI 1.01-1.05, p < 0.001) and high blood pressure (OR 1.02, CI 1.01-1.04, p = 0.01) were associated with development of ESRD, while kidney size at diagnosis was independently associated with ESRD (HR 0.03, CI 0.01-0.72, p = 0.043). Conclusions: In children with RHD, kidney size at diagnosis predicts the likelihood of developing ESRD. [ABSTRACT FROM AUTHOR]