Abnormalities of endocrine function and growth are common following stem cell transplantation in the pediatric/adolescent population. Impaired linear growth and adult short stature are associated with younger age at transplant, use of TBI and prior cranial irradiation, and development of chronic GvHD. Primary hypothyroidism is the most common abnormality of the thyroid and is observed in 10-28% of cases following fractionated TBI. Autoimmune hyperthyroidism has also been described post-stem cell transplant and most often results from adoptive transfer of abnormal clones of T or B cells from donor to recipient. Gonadal dysfunction is extremely prevalent and includes oligo-azoospermia in the majority of males treated with TBI, and primary ovarian failure in most women treated with TBI or Busulfan/Cyclophosphamide. Leydig cell function, however, is retained in most males treated with standard forms of cytoreduction. Many patients demonstrate reduced bone mineral density and are at risk of developing osteoporosis in the future.