Ninety consecutive first-time fiberoptic bronchoscopies (FB) were performed on HIV-infected patients with pulmonary symptoms and radiographic evidence of active pneumonitis. Microbiological data were analysed for acute and long-term prognostic significance. 56/90 (63%) patients had one type of microbiological agent recovered from FB, 22/90 (24%) patients had more types recovered, and 12/90 (13%) patients had no types recovered. Nine patients (10%) died during the acute episode of pneumonia. A prognostic factor of a fatal outcome of the acute episode of pneumonia was concurrent multiple pulmonary infections (p = 0.002), mainly ascribed to patients with Pneumocystis carinii pneumonia (PCP) and concomitant bacterial pneumonia (p = 0.003). Specific microbiological findings at FB did not influence long-term survival of patients, and, when omitting patients who died during the acute episode of pneumonia (n = 9), no difference in survival was observed between patients with a) no agent, b) one type of agent or c) more types of agents recovered from FB. Only non-pulmonary parameters such as CD4-count, haemoglobin and age were found to be prognostic parameters. Thus, increased attention should be paid to co-pathogens presenting in HIV-infected patients with pulmonary infection and appropriate therapy instituted.