We prospectively evaluated lower respiratory tract infections in solid organ transplantation (SOT) patients to determine the microbiologic diagnosis and clinical outcomes. We diagnosed 83 cases of pneumonia, 38 of which were community acquired and 45 were nosocomial. Those with bilateral infiltrates or absence of improvement after 3 days of treatment underwent fiberoptic bronchoscopy. Bacterial pneumonia was the most frequent diagnosis and mixed infection predominated in the nosocomial group (11/45 nosocomial versus 1/38 community). Fiberoptic bronchoscopy with bronchoalveolar lavage had higher diagnostic yield in nosocomial pneumonia (77% versus 47%). Mortality differences between the 2 groups were 58% nosocomial versus 8% community-acquired infections (P < 0.001). SOT patients with nosocomial pneumonia, or those who needed mechanical ventilation, had a high mortality rate and benefits from the fiberoptic diagnostic techniques.