MayerRokitanskyKstnerHauser syndrome is a congenital anomaly in the development of the female reproductive system, the essence of which is a violation of the intrauterine development of the Mllerian ducts, causing complete aplasia of the vagina and uterus. Deviation is a total or partial absence uterus, two upper thirds of the vagina, most often in combination with various anomalies of organs and systems, such as excretory, cardiovascular. Currently, the causes of this pathology are not fully understood studied. According to the World Health Organization, the percentage of hereditary factors intrauterine development disorders is approximately 10 to 25%. It is known that patients with this pathology often suffer from diseases of the urinary system (pyelonephritis). Chronic pyelonephritis is a common pathology in any age group due to excessive growth of the bacterial flora. The main causative agent, most often, are representatives of the intestinal microbiota (Escherichia coli, Enterococcus, Staphylococcus). Determination of the genus and species composition of the intestinal microbiota can serve as one of the diagnostic signs that contribute to the timely correction of the main therapy. Presented clinical case demonstrates a change in the biodiversity of the intestinal microbiota in a patient with MayerRokitanskyKstnerHauser syndrome, which entails timely correction of drug therapy regimens in relation to chronic pyelonephritis and achieving remission. Thus, the study of changes in the composition of the intestinal microflora can become a new criterion in the diagnosis and treatment of this disease at an early stage.