A comprehensive clinical, laboratory, instrumental and morphological study of children with congenital hydronephrosis has been carried out. We compared the clinical features of pyelonephritis at children with primary pyelonephritis and congenital hydronephrosis. Bacterial inflammation was dominated symptom at the children with primary bacterial pyelonephritis, whereas children with hydronephrosis had low-grade clinical changes and significant renal functional impairment. Clinically and prognostically more frequent severe unilateral disease was left-side hydronephrosis. For the first time the morphological changes of junction-ureteral segment at the operated children with congenital hydronephrosis have been analyzed. We've established that the evolution of changes correlates with age. Dysplastic and hypoplastic changes take place mainly in muscle layers in younger 3 years old children, in elder children the phenomenon of atrophy and sclerosis dominates over the other pathologic changes. The hystologic picture depends on lateralization of lesions: dysplasia of muscle layers is on the left side, mucous inflammation--on the right.