We analyzed long-term outcomes and psycho-social aspects in 112 children with malignancies surviving 1 year after hematopoietic stem cell transplantation. At 10 years, overall survival was 7575%, TRM 1874% and relapse 1473%; 10-year cumulative incidence of infections was 3174%, cataract 4474%, pulmonary dysfunction 2074%, bone and joint complications 2975%, hypothyroidism 3674%, cardiac complications 1173% and secondary malignancies 773%. Total body irradiation (TBI) was the most significant risk factor associated with cataract, pulmonary impairment, osteoarticular complications and hypothyroidism. Chronic graft-versus-host disease was associated with higher incidence of pulmonary dysfunction. The number of complications per patient increased with time. Half of the patients had psychological disturbance, 13 signs of depression and 16 a history of eating behavior disorders; 54% of patients with one or more long-term complications had psychological problems. Sixty-nine patients had learning difficulties and 36 achieved normal scholarship. With increased follow-up, development of late effects and of psycho-social disturbance are of major concern. While the use of singledose TBI has now been abandoned, other risk factors are still of concern in the early 2000s.