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Congenital obstructive nephropathy is amongst the main causes of chronic renal failure in children. Early diagnosis and initiation of the treatment will delay progressive renal tubular atrophy and interstitial fibrosis with the loss of nephrons. The aim of this study was to evaluate whether urinary (u) semaphorin-3A (SEMA-3A) and Netrin-1 may be potential biomarkers in children with congenital hydronephrosis due to ureteropelvic junction obstruction (UPJO). The study consisted of 42 children with severe hydronephrosis who needed surgery and two control groups (Control One: 42 children with mild, non-obstructive hydronephrosis; Control Two: 44 healthy children). All children had normal renal function. Urinary semaphorin-3A and Netrin-1 levels were measured in different groups using immunoenzymatic ELISA commercial kits. Compared with Control One and Control Two groups, the preoperative median uSEMA-3A/creatinine (cr.) and uNetrin-1/cr. levels increased significantly in the children with severe hydronephrosis (p < .01). One month after surgery, uSEMA-3A/cr. and uNetrin-1/cr. levels had decreased significantly in the children with severe hydronephrosis (p < .01), but were still higher than those in both control groups (p < .05). Receiver operator characteristic (ROC) analyses revealed a good diagnostic profile for uSEMA-3A and uNetrin-1 in terms of identifying children with a differential renal function of <40% [area under the curve (AUC) 0.825 and 0.745, respectively]. Our results indicate that increased concentrations of uSEMA-3A and uNetrin-1 are found in urine from children with severe hydronephrosis and that their concentrations are related to the degree of obstruction.