Bronchiolitis obliterans (BO) is a severe pulmonary complication of allo-SCT. This study evaluated the incidence of BO in patients undergoing allo-SCT in Hospital Universitário da Universidade Federal do Paraná, risk factors for developing this complication and prognostic factors for those patients who developed this entity. The study included 1286 patients transplanted between 1979 and 2009 who survived for 100 days or more. We diagnosed 53 cases of BO. The cumulative incidence was 2.9% in 1 year and 3.7% in 3 years. Among patients with chronic GVHD, the cumulative incidence at the same intervals was 8.4% and 9.9%, respectively. The median time between transplantation and diagnosis of BO was 260 days (49-3877 days). In the multivariate analysis the risk factors for BO were female donor, older recipients and acute GVHD. The main prognostic factor was the severity of pulmonary impairment. Patients who developed BO earlier than 260 days had a worse prognosis than those who did so later. At least 80% of deaths were directly related to BO.