The current prospective study dealt with clinical outcome associated with pulmonary and cardiac late effects of AuHCT in children with malignancies. We prospectively evaluated 58 children, utilizing pulmonary function tests and cardiac shortening fraction, performed in pre-AuHCT phase and then annually. The overall five-yr survival was 68%. The five-yr cumulative incidence of lung and cardiac function impairment in survivors was 21% in both cases. None of the patients presented with restrictive or obstructive pulmonary pathology at the last follow-up and performance status for all survivors, ranged from 90% to 100%. The cumulative incidence of non-relapse mortality was 12.6% (range 6.3-25.3%), whereas relapse mortality was 19.7% (range 11.6-33.5). In conclusion, our study shows no significant deterioration in post-AuHCT pulmonary and cardiac function and in particular, no negative impact of lung and heart late effects on performance status and non-relapse mortality.