Strengths of the present study are its prospective and multicentre design, the large number of consecutive hospitalized patients with pneumonia included in both periods, and the comprehensive clinical data collection. In addition, this study was conducted in geographically diverse settings across Spain, a feature that improves the external validity of the results. However, our study has several limitations that should be acknowledged. We only examined hospitalized patients with influenza A (H1N1) 2009 pneumonia and cannot make assertions about other populations. Hospital criteria decisions were not standardized and we did not have information regarding the percentage of patients tested by PCR for H1N1 influenza virus in each study period. Moreover, we have no data regarding the percentage of patients with influenza A (H1N1) 2009 pneumonia treated by primary-care physicians. Likewise, we could not calculate incidence rates and the differences between study periods. However, according to data provided by the Spanish Influenza Surveillance System (http://vgripe.isciii.es/gripe/inicio.do), the highest incidence of influenza cases during the pandemic period (2009) were in weeks 43–47 (372 cases/100 000 inhabitants) and during post-pandemic influenza season period (2011) were in weeks 2–3 (230 cases/100 000 inhabitants). Finally, serum samples to determine antibodies against influenza A (H1N1) 2009 virus were not obtained and we did not perform testing to identify emerging new antigenic virus.