Introduction The aim was to study the characteristics and case severity of patients hospitalized for influenza with a pandemic strain at a German tertiary care university hospital in 2009/10 and 2010/11 and to compare them to two previous influenza seasons. Methods An observational study of all patients hospitalized for laboratory-confirmed influenza during the last four influenza seasons at Regensburg University Hospital was undertaken. Results During the last four seasons, a rising number of patients were admitted due to influenza (4 in 2007/8, 16 in 2008/9, 27 in 2009/10, and 55 in 2010/11). Patients seen in the last two seasons were younger (median age 63 years in 2007/8, 52 years in 2008/9, 42 years in 2009/10, and 48 years in 2010/11) (p = 0.046) and presented with a lower rate of major comorbidities (75 % in 2007/8, 62.5 % in 2008/9, 37 % in 2009/10, and 47.3 % in 2010/11). The pandemic and post-pandemic seasons were characterized by a high rate of seriously ill patients with longer hospitalizations (11 days in 2007/8, 7 days in 2008/9, 22 days in 2009/10 and 2010/11) (p = 0.004) and higher rates of intensive care unit (ICU) admission (25 % in 2007/8, 18.8 % in 2008/9, 66.7 % in 2009/10, and 52.7 % in 2010/11) (p = 0.003) and mechanical ventilation (25 % in 2007/8, 6.3 % in 2008/9, 63 % in 2009/10, and 49.1 % in 2010/11) (p < 0.001). Extracorporeal membrane oxygenation (ECMO) was necessary in 33.3 % of patients in 2009/10 and 25.5 % in 2010/11. We had six fatalities in both pandemic and post-pandemic seasons. Conclusion Compared to seasonal influenza, we observed even more so in the post-pandemic than the pandemic season a higher number of younger patients, with less serious comorbidities often showing a very severe course.