With the increasing use and success of BMT, larger numbers of children survive transplantation. Still, cancer treatment in children causes damage to the endocrine glands, often inducing growth deficiency, pubertal delay and thyroid dysfunction. This paper will deal with some of the most common endocrine disorders related to BMT in the pediatric population. Irradiation is the major contributor for growth impairment after BMT, acting through lesion to epiphyseal growth-plate, gonadal damage with delayed or precocious puberty, hypothyroidism, and growth hormone insufficiency. Gonadal dysfunction can be induced both by a direct injury to the gonads (irradiation, gonadotoxic agents) causing primary hypergonadotropic-hypogonadism, and with less frequency, by neuroendocrine injury to the hypothalamo-pituitary axis causing hypogonadotropic-hypogonadism. It seems that both doses of chemotherapy and of irradiation used by different regimens, fractionation of irradiation, and age at the time of BMT are the most important factors when we deal with toxic endocrine late-effects in long term survivors. In order to improve the quality of life of each single patient who receive BMT, and without inflicting the success-rate of this procedure, we recommend a life-long surveillance to prevent or to treat symptoms and disorders caused by hormone deficiencies, and we also advocate for a multidisciplinary team-approach that includes an endocrinologist consultant.