Since the 1980s, hematopoietic stem cell transplantation (HSCT) has been performed for malignant and non-malignant disorders leading to increasing numbers of long-term survivors. Some of them develop long-term posttransplantation complications, among them endocrine complications that arise many years after HSCT and demand to be treated till the end of patients´ life. In the paper "classical", observed several years after HSCT had been used as a treatment procedure, endocrine complications are discussed and the review of literature regarding this problem is presented. Thyroid dysfunction, disorders of somatic and sexual development are presented in details. Gonad dysfunction with the problem of fertility disturbances is reported. The paper presents the etiopathogenesis, methods of prevention, as well as treatment and the results of the treatment of these endocrine complications after HSCT. Moreover actual recommendations for screening and prevention of endocrine complications in long-term HCT survivors are presented.