We used data from BioSense, a national electronic surveillance system, to describe pneumonia in hospitalized patients with influenza-like illness (ILI). Ninety-five hospitals from 20 states reported ICD-9-CM-coded inpatient final diagnosis data during the study period of September 2007 to February 2010. We compared the characteristics of persons with and without pneumonia among those with ILI-related hospitalizations. BioSense captured 26987 ILI-related inpatient hospitalizations; 8979 (33%) had a diagnosis of pneumonia. Analysis of trends showed highest counts of pneumonia during the 2007–2008 season and the second 2009 pandemic wave. Pneumonia was more common with increasing age. Microbiology and pharmacy data were available for a subset of patients; 107 (5%) with pneumonia had a bloodstream infection and 17% of patients were prescribed antiviral treatment. Our findings demonstrate the potential utility of electronic healthcare data to track trends in ILI and pneumonia, identify risk factors for disease, identify bacteraemia in patients with pneumonia, and monitor antiviral use.