Patients who undergo allogeneic hematopoietic SCT (HSCT) are prone to pulmonary infections. Between 1998 and 2004, a total of 450 patients underwent HSCT at Karolinska University Hospital, Huddinge. Pneumonia was diagnosed in 167 patients (37%), including 42 children. Bronchoalveolar lavage (BAL) was performed on 68 occasions in 57 patients (six children). In 110 patients (36 children) with pneumonia, BAL was not performed. BAL contributed to the diagnosis in 43 cases (63%) and to relevant findings in 53 cases: bacteria (n=13, 24%), viruses (n=28, 53%) and fungi (n=12, 23%). In 25 cases BAL was negative. In 15 of these cases, BAL was performed >or=4 days after chest X-ray, and in four cases not in the same segment as the infiltrations. The median time between radiographic findings and positive BAL was 2 (0-15) days, and a negative BAL 6 (1-30) days (P<0.001). Antimicrobial treatment was administered to 79% patients with positive findings, and to 92% with negative findings at the time of BAL. No serious complications due to the procedure were reported. BAL resulted in a changed treatment in 32/68 (47%) episodes of pneumonia. To conclude, BAL is a safe and useful diagnostic procedure that should be performed early after the onset of pneumonia following allogeneic HSCT.