BACKGROUND: Bronchoscopy with bronchoalveolar lavage (BAL) and respiratory tract biopsies are important tools for diagnosing fungal infections in children with cancer and hematopoietic stem cell transplant (HSCT) recipients. Our objective was to evaluate the impact of BAL and respiratory tract biopsies on the management of suspected fungal infections in oncology and HSCT patients. PROCEDURE: We retrospectively reviewed the medical records of oncology and HSCT patients with possible, probable, or proven fungal infection of the respiratory tract and determined whether BAL or biopsy following computed tomography (CT) prompted a change in management. RESULTS: Among 101 patients (0.5-29 years of age), 24 underwent a BAL and 31 had biopsies (27 lung and 4 sinus). The remaining 46 patients had CT scans only. Of these, there were radiographic findings suggestive of a fungal infection in 38 patients (83%). Thirty of these 38 patients (79%) had a change in management. BAL provided a diagnosis in 6 of 24 patients (25%). There was a change in management in 2 of the 6 (33%). Respiratory tract biopsy provided a diagnosis in 12 of 31 patients (39%). Biopsy results led to a change in management in 4 of the 12 patients (33%). Significant postoperative morbidity attributed to biopsy occurred in 3 of 31 patients (10%); 2 patients had pneumothorax requiring chest tube and intubation and a patient had prolonged intubation. CONCLUSION: BAL and biopsy in children with an oncological diagnosis or those undergoing HSCT only infrequently lead to changes in management in the era of empiric therapy with broad-spectrum anti-fungal agents. Pediatr Blood Cancer 2015;62:1579-1586. (c) 2015 Wiley Periodicals, Inc.