Flexible bronchoscopy is a useful diagnostic procedure in patients with respiratory failure due to unexplained pulmonary infiltrates, but its safety and usefulness in ventilator-dependent patients with severe thrombocytopenia have not been established. A retrospective review of the medical records of all patients who underwent bronchoscopy while receiving mechanical ventilation support at Samsung Medical Centre, Seoul, Korea between January 2002 and July 2006 was conducted. The medical records of 37 patients with severe thrombocytopenia (platelet count <50,000 /microl) at the time of bronchoscopy were analysed. Mean platelet count was 27,300+/-12,500 /microl. The most common underlying condition was haematologic malignancy, which occurred in 21(56.7%) patients, followed by severe sepsis in five (13.6%) and post-liver transplantation complications and autoimmune disease in four each (10.8%). The procedures performed were bronchoalveolar lavage in 33 patients, washing in three and transbronchial lung biopsy in five. Two patients died within 24 hours of completing the procedure. In patients surviving longer than 24 hours, there was no significant decline in oxygenation index (PaO2/FiO2), sequential organ failure assessment score or simplified acute physiological score II after the procedure. Lung compliance significantly decreased at two hours post-bronchoscopy but recovered to the pre-bronchoscopy level by 24 hours. Intensive care unit mortality was 51.4% (19 of 37 patients). Bronchoscopy was helpful in confirming the diagnosis in 17 patients (45.9%). Therapeutic modifications were made in 14 patients (37.8%) after bronchoscopy. Severe thrombocytopenia per se should not preclude bronchoscopy, even in patients receiving mechanical ventilation.