The aim of the present study is to evaluate the epidemiology, etiology and prognosis of pneumonia in lung transplant (LT) recipients. This is a prospective, multicenter study of a consecutive cohort of LT recipients in Spain. From September 2003 to November 2005, 85 episodes of pneumonia in 236 LT recipients were included (incidence 72 episodes per 100 LT/year). Bacterial pneumonia (82.7%) was more frequent than fungal (14%) and viral pneumonia (10.4%). The most frequent microorganisms in each etiological group were Pseudomonas aeruginosa (n = 14, 24.6%), CMV (n = 6, 10.4%) and Aspergillus spp. (n = 5, 8.8%). Incidence of Aspergillus spp. and CMV pneumonia is lower than previously reported, probably due to the spread of universal prophylaxis. Pneumonia caused by viruses appeared significantly later than pneumonia due to gram-negative bacilli, fungi and those without known etiology (p < 0.01, p = 0.03 and p = 0.02, respectively). The routine use of ganciclovir has changed the natural history of CMV infection, so that pneumonia appears later, once prophylaxis is suspended. The probability of survival during the first year of follow-up was significantly higher in the multivariate analysis in LT recipients who did not have a pneumonia episode compared with those that had at least one episode (p < 0.01).