We report a case of bronchiolitis obliterans (BO) associated with allogenic peripheral blood stem cell transplantation for acute leukemia. On inspiratory and expiratory chest computed tomography (CT), characteristic findings for BO, such as air-trapping, mosaic attenuation or bronchial wall thickening were not clearly observed. However, ventilation-perfusion lung scans of the chest demonstrated multiple matched defects, which suggested severe obstructive airway disease. In the diagnosis of BO after stem cell transplantation, lung scans should be recommended when representative findings are not obvious on chest CT.