Today, the association of gut microbiota with external genital endometriosis (EGE) is of special scientific interest. The study was aimed to assess alterations of the gut microbiota taxonomic composition and explore their correlations with plasma levels of IL6, IL8 and TNFα at the species level in patients with EGE. The crosssectional comparative study involved 50 patients with EGE (index group) and 50 healthy women (control group). The changes in the gut microbiota taxonomic composition and plasma levels of IL6, IL8 and TNFα were assessed. A significant decrease in the abundance of such species, as Coprococcus catu (р = 0.009), Turicibacter sanguinis (р = 0.008) and Ruminococcus gnavus (р < 0.001), along with the increase in the abundance of Eubacterium ramulus (р = 0.040), Bacterioides dorei (р = 0.001), Prevotella divia (р = 0.008) and Shigella flexneri (р < 0.001) were found in the gut microbiota taxonomic composition in patients with EGE. Significant correlations between the IL6 levels and the abundance of Turicibacter sanguinis (r = –0.92; р = 0.001), IL8 levels and the abundance of Shigella flexneri (r = 0.72; р < 0.001), TNFα levels and the abundance of Prevotella divia (r = 0.77; р = 0.001) were revealed. The findings add to the available literature data on the features of gut microbiota alterations and their association with some inflammation biomarkers in individuals with EGE, which can justify further research in this area and probably open up new approaches to treatment of the disease.