Kazakhstan is an unfavorable endemic zone on thyroid diseases. Autoimmune thyroiditis is one of threatening diseases for the women reproductive system. It is especially important, that AIT often combines with gynecological and with obstetric pathology. In turn the level of inflammatory diseases of the pelvic organs in Kazakhstan remains very high.Later beginning of treatment conduces to the heaviest consequence: sterility. With the help of hormonal contraceptives it becomes possible to affect on sexual hormones that regulate exchange processes and possess an antimicrobial action. A hormonal contraception does not cause negative influence on maintenance of TSH and T4 in the serum of blood, what is more, causes the immunosuppressive influence on the anti-TPO, anti-Tg level of, has a favorable influence on the flow of AIT and equilibrates the state of health. Thus, a hormonal contraception in combination with basic therapy of pelvic inflammatory diseases with autoimmune thyroiditis does not cause adverse influence on thyroid hormones and forms a normal vaginal biotope.