Background. Hepatitis C is one of the major problems of nosocomial infections associated with blood transfusions, administration of blood products, and medical manipulation with invasive diagnostic and therapeutic purposes. The purpose of our study was to establish population level of taxons of colon microbiota in patients with chronic hepatitis C. Materials and methods. 72 samples of colon content of patients with chronic hepatitis C, including 44 women, 28 men aged 21 to 53 years (average age (37.5 ± 1.7) years old) underwent microbiological investigation. Results. The study showed that the population of Bifidobacterium spp. in the colon lumen of patients with chronic hepatitis C decreased by 41.28 %, Lactobacillus spp. by 41.15 %, the coefficient of quantitative domination by 2.07 and 2.22 times, the significance coefficient by 3.25 and 3.36 times, respectively, that contributes to the population level increasing, coefficients of quantitative domination and significance of Bacteroides spp. by 65.01 % and 24.94 %, respectively, that means increased population level bacteria species of Escherichia and Enterococcus by 52.21 and 26.48 %, respectively, Peptostreptococcus spp. by 57.43 %, Clostridium spp. by 2.03 times. Conclusion. In colon lumen of patients with chronic hepatitis C there is formed distinct deficiency of autochthonous obligate Bifidobacterium spp. by 41.28 %, Lactobacillus spp. by 42.15 %, increased concentration of Bacteroides spp. in biotope by 65.01 %, Peptostreptococcus spp. by 57.43 %, Clostridium spp. by 2.03 times, and Escherichia bacteria by 52.21 % and Enterococcus by 26.48 %. Dysbiosis/dysbacteriosis of II–III stages (80.56 %) was diagnosed by the changes of population level of main, additional and accidental colon luminal microbiota in majority patients with chronic hepatitis C.