Fibreoptic bronchoscopy with bronchoalveolar lavage (BAL) is used for clinical investigation and research into pulmonary complications of stem cell transplantation. Adverse effects of BAL are common in neutropenic patients with lung disease; there are few data on its safety when used routinely in transplant recipients without lung impairment. We describe the complications and usefulness for infection surveillance of routine BAL pre-transplantation and during neutropenia. Thirty-three patients before autologous or allogeneic BMT or PBSCT (B1) and 24 during post-transplant neutropenia (B2) underwent BAL; patients with pulmonary disease were excluded. Subjects were monitored for adverse effects, and BAL fluid was examined for pathogens. Complications of B2 were compared with events seen in 35 neutropenic patients who did not undergo BAL (C). Eighteen percent B1 and 33% B2 subjects showed complications of BAL. Fever occurred in 12% B1 and 26% previously afebrile B2 subjects, compared to 11% of C (P = 0.3). Epistaxis occurred in one B2 subject and two C. Potentially pathogenic organisms were isolated from 18% B1 and 13% B2 BAL fluids; none caused later respiratory infection. Bronchoscopy and BAL pre- and post-transplant had acceptable safety for a research procedure, but were not clinically helpful for infection surveillance.