Late effects of bone marrow transplantation are of clinical concern as more patients survive the early phase after transplantation and remain free of their original disease. Late effects express themselves as structural or functional impairment of organs or tissues or as neoplastic growth secondary to the primary treatment. Non-neoplastic late effects affect growth and development of children, endocrine and reproductive function, and the function of eyes, lungs, kidneys and other organs. Secondary neoplasms comprise malignant lymphoma and leukaemia, many of them in donor cells, that occur early after transplantation. The incidence of solid tumours is increased years after transplantation. At present the risk of secondary neoplasms after transplantation appears not to be different from that of intensive chemoradiotherapy without transplantation. In contrast to conventional chemoradiotherapy secondary malignancies of the host's haemopoiesis are rare due to the myeloablative conditioning. The incidence of solid tumours may increase as more patients survive more than a decade after transplantation.