Abstract Background and Aims In view of the fact that the human microbiota varies depending on many factors, including comorbid pathology, it seems reasonable to investigate the gut microbiota in patients with chronic kidney disease and its likely relationship with markers of systemic inflammation. To reveal the relationship between some biomarkers of inflammation with changes in the composition of the intestinal microbiota in patients with chronic kidney disease. Method The study included 85 patients with CKD C 2-4. The average age of the patients was 52 ± 4 years (48 men and 37 women). The control group consisted of 30 healthy volunteers aged 50 ± 3 years, 15 men and 15 women, comparable to the main group in terms of sex and age. Blood samples were taken using standard methods. GFR was assessed using the CKD-EPI formula (2011). In addition, biomarkers such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α) were evaluated. Bacteriological examination of feces was carried out in the bacteriological laboratory.Markers of systemic inflammation were assessed based on an increase in the level of leukocytes (> 11 × 109 / L), C - reactive protein (> 5.0 mg / L) by immunoturbodimetric method, fibrinogen (> 4.0 g / L), as well as interleukin 6 by enzyme immunoassay. Differences between groups were considered statistically significant at p`0.05; correlation analysis was performed using Spearman's nonparametric rank correlation method. Results Analysis of fecal matter showed a deficiency of Bifidobacterium bacteria (<108 CFU) in the examined patients. In addition, the examined patients showed an increase in the number of Echerichia (> 108 CFU). According to the results of the study, in the group of CKD patients, the level of inflammatory markers was higher (CRP-55%, IL-6-60%, leukocytes 62%) than in the control group (CRP-45%, IL-6-40%, leukocytes 38% ). In men, the IL-6 index was higher than in women. The results of the study demonstrated that in patients with CKD, an imbalance of the intestinal microbiota is combined with an increased level of CRP, IL-6, and leukocytes. Conclusion The study of markers responsible for pro-inflammatory effects in the body showed that indicators such as IL-6, CRP, fibrinogen showed a significant correlation with the composition of the microbiota in patients with CKD.