This study was undertaken to evaluate in a primarily pediatric population whether the late effects of bone marrow transplantation (BMT) on pulmonary function in patients having undergone the procedure for treatment of acute leukemia or lymphoma are worse than that of patients having undergone transplant for treatment of aplastic anemia. Forty-six patients were studied. We did not demonstrate statistically significant differences in group mean forced expiratory flow in one second/forced vital capacity (FEV1/FVC) and percentage predicted forced expiratory volume in one second (FEV1), forced vital capacity (FVC), forced expiratory flow at 25-75% of the forced vital capacity (FEF25-75) and total lung capacity (TLC) values between the two groups of patients before BMT and to 7 years post-transplant. Individual patients with pulmonary function abnormalities were identified. Furthermore, there were no significant differences between the two study groups or within the group of patients with aplastic anemia from pre-transplant to 9-12 months and from pre-transplant to 18-24 months after BMT. However, within the group of patients treated for acute leukemia or lymphoma, there was a significant decline in the group mean percentage predicted FVC (p = 0.0001), FEV1 (p = 0.0006) and FEF25-75 (p = 0.0063) from pre-transplant to 9-12 months and in the FVC (p = 0.004) and FEV1 (p = 0.0006) from pre-transplant to 18-24 months after BMT. The greater decline in the FVC relative to the FEV1 suggests the development of a restrictive process in this group of patients.