BACKGROUND: Bronchiolitis obliterans (BO) is a severe complication after allogeneic hematopoietic stem cell transplantation with an unfavorable prognosis. Lung biopsy remains the gold standard for diagnosis. DESIGN AND METHODS: In this retrospective single center study we describe 33 patients who underwent biopsy for suspected BO. RESULTS: Ten patients had constrictive BO (CBO); 9 had lymphocytic bronchiolitis (LB), characterized by lymphocytic infiltration of the bronchioles. Six additional patients (4, CBO; 2, LB) had concomitant infection; 8 had other pathological diagnoses. Seven patients with CBO and three with LB met the NIH consensus BOS definition criteria. Further seven patients with histologically confirmed CBO did not meet the consensus definition - four of them because of concomitant airway infection. At diagnosis, there was no significant difference between the CBO and LB groups in clinical presentation, pulmonary function tests (median FEV1 at baseline, 90.4% and 99% predicted; at time of VATS, 55.1% and 60.8% for CBO and LB groups, respectively), and chest scans. Treatment was similar in both groups but outcome was different depending on histological findings. FEV1 significantly improved in LB patients compared with CBO patients. Survivals at one and three years were 77% (±12%) and 60% (±14%) for CBO-patients and 91% (±9%) for LB-patients (p = 0.028). CONCLUSION: Lung biopsy in patients with suspected BO enables better characterization of the pattern of BO syndrome. In contrast to CBO, LB is associated with a good long-term prognosis.