A 6-year-old female patient who underwent bone marrow transplantation because of Fanconi anaemia presented with fever, dyspnoea and cough 17 days after the procedure. The physical examination revealed diffuse crackles. Chest radiographs demonstrated diffuse alveolar opacities in both lungs. High-resolution CT showed a diffuse and bilateral lung lesion characterized by multifocal areas of air-space consolidation associated with ground-glass attenuation and small centrilobular nodules. The culture of the material obtained with bronchoalveolar lavage only demonstrated growth of Stenotrophomonas maltophilia. The patient rapidly presented respiratory insufficiency and death in the same day.