Management of pulmonary complications after hematopoietic stem cell transplantation (HSCT) often includes bronchoalveolar lavage (BAL), but the diagnostic yield of BAL remains unclear in pediatric HSCT patients. We reviewed the records of 78 allogeneic and 11 autologous transplant recipients who underwent BAL after HSCT at St. Jude Children's Research Hospital (1990-2002). We analyzed donor and recipient information, clinical variables, adverse events during bronchoscopy, outcome, and medical management at the time of the procedure to determine the diagnostic yield of BAL and factors that affect its success. Seventy-eight allogeneic and 11 autologous transplant recipients underwent BAL at a median of 68 days (range, 6-528 days) and 23 days (range, 6-705 days) after HSCT, respectively. The median age at the time of BAL was 12.2 years (0.8-23.5 years) in allogeneic patients and 16.9 years (4.8-26.2 years) in autologous patients. The most common indications for BAL in both populations were fever, hypoxia, and abnormality on chest auscultation. BAL identified an etiology in 53 allogeneic (67.9%) and 7 autologous (63.6%) patients (BAL positive); only 1 etiology was identified in 30 of the 53 allogeneic patients (56.6%). The most common finding was bacterial infection in both allogeneic (59.0%) and autologous (71.4%) patients. Of 39 allogeneic patients who had concurrent extrapulmonary infection, 30 (76.9%) had a positive BAL. Seven (9.0%) allogeneic patients experienced hypoxia (generally transient) during bronchoscopy. Approximately 68% of those with a positive BAL were receiving immunosuppressive therapy, whereas 96% of patients with a negative BAL were receiving immunosuppressive therapy (P = .008). Further, 26.4% of the BAL-positive cohort had grade II-IV acute graft-versus-host disease (aGVHD), whereas 60% of the BAL-negative group had grade II-IV aGVHD (P = .004). In our experience, the safety and diagnostic yield of BAL in this set of patients is relatively high, but the likelihood of informative findings is reduced among allogeneic recipients with grade II-IV aGVHD and those receiving immunosuppressive therapy.