The purpose of the investigation was to study the quantitative and qualitative composition of colon microflora in system connective tissue diseases and system vasculites. The authors studied colon microflora in patients with systemic lupus erythematosus, systemic scleroderma, nodular polyarteritis, and hemorrhagic vasculitis. The structure of symbiotic interrelations between microorganisms participating in the formation of colon microbiocenosis was determined. Colon microflora was found to be disordered in terms of its qualitative and quantitative composition. The predomination of anaerobic microorganisms was decreased, while the role of conditionally pathogenic bacteria was increased. The number of lactobacteria was significantly lowered; bifidobacteria and bacteroids were found frequently, while their number was substantially lowered as well. Conditionally pathogenic microorganisms and bacteria with hemolytic activity acquired high significance in the forming of the colon microbiocenosis of the patients. The frequency of the isolation and the density of colon colonization with staphylococci and conditionally pathogenic enterobacteria were significantly increased. General trends and peculiarities of changes in the quantitative and qualitative composition of colon microflora in some rheumatic diseases were determined. The data on the peculiarities of the colon microbiocenosis in these patients may be used to substantiate methods of complex therapy including correction of dysbiotic disturbances.