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Aim: to study the distribution of alleles and genotypes of polymorphic markers for immunoregulatory cytokines in the development of chronic pyelonephritis and its clinical variants. Patients and Methods: in this study we analyzed a sample of 99 patients with chronic pyelonephritis. The average age of the patients was 8,01±3,26 (3,00–15,00) years. The study of gene polymorphisms was performed using PDRF analysis. For PCR were used primers structures and genotyping conditions described in the literature. Results: the analysis of associations of 2 loci in the genes of cytokines with different complex phenotypes of chronic pyelonephritis demonstrated that A2 allele and genotype A2A2 of IL1RN*VNTR polymorphism is associated with chronic pyelonephritis, vesicoureteral reflux, secondary pyelonephritis, renal dysfunction, infection with Escherichia coli and Klebsiella. Genotype A2A2 of gene IL1RN*VNTR and allele A2 of gene IL1RN*VNTR are associated with impaired renal function OR =3,07 (p =0,001). The highest risk of chronic renal failure development is associated with A1A2 genotype (OR =22,94; p=0,001). Conclusions: the discovered associations require further confirmation on larger samples and various ethnicities.