Gonadal damage, often associated with irreversible failure, is an invariable effect of high-dose myeloablative chemotherapy used for allogeneic or autologous bone marrow transplantation. Although not life threatening, the psychological consequences are significant. Therefore semen cryopreservation is advisable prior to initial therapy, but oocyte storage is not yet possible and embryo cryopreservation seldom feasible. Treatment protocols should be carefully selected to maximise cure rates whilst limiting injury to the reproductive system. Involvement of a reproductive endocrinologist is thus ideal from presentation, and certainly necessary pretransplant and for long-term follow-up in order to provide the endocrine assessment, counselling and fertility management which are essential for adequate transplant care. Improvement in bone marrow transplant technology and more rigorous patient selection have resulted in a higher proportion of long-term survivors. This has increased the awareness of long-term effects, such as gonadal failure, which may become apparent several months or years after transplantation. Premature ovarian and testicular failure may be overlooked by physicians managing the life-threatening disease, but for patients, the physical, emotional, psychological and social consequences of functional castration consequent on high-dose therapy can be devastating. The pathophysiology, diagnosis and management of gonadal failure are reviewed here.