Lung scintigraphy has been used to evaluate the degree of pulmonary hypoplasia in infants with congenital diaphragmatic hernia (CDH). However, the relationship between lung scintigraphy and long-term outcome of CDH remains unclear. The aim of this study is to determine whether lung scintigraphy correlates with long-term pulmonary morbidity and nutritional status in survivors of CDH. Consecutive 31 survivors of CDH were enrolled in this study. The initial scan was performed at 1-2 months when the patients were ready for discharge and the follow-up scan was performed following an approximately 1-year interval. The regional ventilation and perfusion were evaluated using (133)Xe-inhalation and intravenous (99m)Tc-MAA injection, respectively. The ventilation and perfusion of the ipsilateral lung was expressed as a percentage of that of the contralateral lung. Physical growth at 1 and 2 years, and pulmonary morbidity were reviewed from medical records. The ventilation and perfusion of the ipsilateral lung at the follow-up scan increased significantly from those at the initial scan. Ten patients had pulmonary morbidity. The ventilation and perfusion of the ipsilateral lung was significantly lower in the patients with pulmonary morbidity compared to the patients without pulmonary morbidity. The initial ventilation and perfusion of the ipsilateral lung were strongly correlated with body weight at 1 and 2 years (ventilation: R = 0.503, P < 0.01; perfusion: R = 0.760, P < 0.0001). These results suggest that lung scintigraphy is useful to predict long-term pulmonary morbidity and poor nutritional status in survivors of CDH.