Species composition and population level of microflora of the cavity of the large intestine in 44 patients with hypothyroidism have been studied. The dysbiosis of the first degree – in 1 patient, the second degree – in 1 patient, the third degree – in 8 patients and the fourth degree – in 34 patients have been established. Imbalance developed at the expense of eliminations and deficiency of autochthonous anaerobic, obligatory bacteria (bifid bacteria, lacto bacteria), contaminations of the large intestine by enterotoxigenic, enteropathogenic and hemolytic Escherichia, conventionally pathogenic enterobacteria and an increase of the number of the bacteriodes, peptococcus, peptostreptococci, clostridia, staphylococci and yeast-like fungi of the Candida type.