Endocrine disorders are an extremely urgent medical and social problem of modern society. Changes in the thyroid gland activity cause violations of the regulation of metabolism in periodontal tissues. Expressed clinical signs of periodontal tissues inflammation directly depend on the severity and duration of disorders of the functional state of the thyroid gland. The purpose of this study was to describe the ultrastructural changes of periodontal tissues under the conditions of experimental periodontitis in combination with hypothyroidism. To model periodontitis lipopolysaccharide was injected into the gum tissue of rats. The experimental thyroid gland hypofunction was simulated using intragastrical administration of mercazolyl. To confirm the state of hypothyroidism we determined the content of free thyroxine, free triiodothyronine and thyroid-stimulating hormone. Submicroscopic studies revealed profound destructive-degenerative changes in all components of the periodontium. Changes in periodontal tissues in experimental hypothyroidism are stereotyped: dystrophic, atrophic and destructive changes in parenchymal structures, mucinous edema of the stroma, mild reparative processes. Thus, it can be concluded that during experimental periodontitis in combination with hypothyroidism, there are violations of the functioning of all the components of the vessels of the periodontal microcirculatory channel. This is manifested by damage and deformation of the blood vessel wall with desquamation of the endothelium, edema, thinning of the basement membrane, stasis, thrombosis and spasm. Also, significant destruction and lysis of fibrous structures and components of the connective tissue amorphous substance in the lamina propria of the attached and free part of gums and periodontium are characteristic.