Pediatric hydronephrosis may correspond to very different clinical situations, ranging from fully benign reversible dilatation to severe obstructive nephropathy. The genetic research is difficult, mainly because the condition is probably polygenic and the embryology of the urinary system is very complex and depends on a multifaceted interaction of genetic and environmental factors. Molecular biology has gained new insights in the complicated urinary system and in the mechanisms of obstructive nephropathy. Some mediators (tumor growth factor, tumor necrosis factor, renin angiotensin system, etc.) could be considered molecular markers of obstruction and it has been proposed to introduce them in clinical decision making, in order to make an accurate selection of patients needing surgical correction. Scintigraphy has been a standard procedure in the management of pediatric hydronephrosis for decades and has been used in many clinical studies designed to evaluate the role of selected molecular markers in clinical settings. The relationships between scintigraphic parameters and molecular mediators seems promising, in particular for the evaluation of the Reanin Angiotensin System, which plays many roles in the natural history of pediatric hydronephrosis. Angiotensin up-regulation is a turning point in many pediatric hydronephrosis and can be unveiled by captopril scintigraphy, which allows a timely diagnosis of obstruction, before irreversible parenchymal injury and loss of renal function.