Modern scientific data and the emergence of new opportunities for the development of pediatrics and nephrology are inextricably linked with medical genetics, the role of which is especially important for understanding the etiology and pathogenesis of many diseases of the urinary system. In 35–80 % of children with diffuse connective tissue diseases, kidney damage is formed, which is one of the leading causes of comorbidity of pathology and mortality of patients. Modern genetic research will allow not only to decipher the nature of diseases but also to scientifically substantiate adequate therapy. The active development of methods for the molecular diagnosis of kidney diseases opens up a large section of medicine, which can be called "molecular nephropathology". Further study of kidney diseases from the standpoint of molecular biology will allow us to take a fresh look at the pathogenesis of many diseases and solve a number of problems from the standpoint of personalized therapy, which takes into account the genetic characteristics of the patient. The active development of genetic research in nephrology has led to an understanding of the role of genetic mutations and polymorphisms leading to the occurrence of nephropathies in children. Correct clarification of the causes of the development of the disease can radically change the tactics of managing a patient by a nephrologist and rheumatologist. Determination of the genetic cause of the development of nephropathy is important in children since it justifies the need to examine other family members, it will allow predicting the risk of developing kidney pathology in diffuse connective tissue diseases, which is very important, predicting the response to immunosuppressive therapy. The development of molecular diagnostic methods is increasingly opening up prospects for a personalized approach to the study of pathology at various levels of interaction; these achievements provide a qualitative assessment of DNA, RNA, proteins, and their metabolites, which makes it possible to determine new biomarkers. The article deals with gene polymorphisms in secondary nephropathies in children with diffuse connective tissue diseases (systemic lupus erythematosus, systemic microthrombovasculitis, rheumatoid arthritis).