We retrospectively reviewed the results of serial pulmonary function tests (PFT) after allogeneic bone marrow transplantation (BMT) performed in 80 children at a single institution over a 16-year period. We looked for associations linking PFT results to graft-versus-host disease (GVHD), conditioning regimen (total body irradiation (TBI) vs busulphan), and cytomegalovirus immune status. The median follow-up after BMT was 4 years. At 2 years after BMT, significant declines were found in forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1), as compared to baseline. Both FEV1 and the FEV1/FVC ratio showed significantly greater reductions in the group conditioned with busulphan (n=22) than in the group conditioned with TBI (n=49) and were significantly lower in the patients with (n=16) than without (n=64) chronic GVHD. Busulphan may be associated with greater long-term lung toxicity than TBI. The relevance of this finding to selection of conditioning regimens for BMT should be examined in the light of the overall pattern of side effects. Chronic GVHD was associated with airway obstruction.