The mortality in Germany caused by the 2009 pandemic influenza A(H1N1) seems to have been one of the lowest in Europe. We provide a detailed analysis of all 252 fatal cases of confirmed infection with the pandemic virus notified between 29 April 2009 and 31 March 2010. The overall mortality was 3.1 (95% confidence interval (CI): 2.7 to 3.5) per one million inhabitants. We observed an increase in the case fatality rate of notified cases over time; notified cases aged 60 years or older had the highest case fatality rate (2.16%; 95% CI: 1.61 to 2.83; odds ratio: 5.4; p<0.001; reference group: 35–59 years). The median delay of four days (interquartile range (IQR): 2–7) between symptom onset and antiviral treatment was significantly longer in fatal cases than for non-fatal cases (median: two days (IQR: 1–3; p<0.001). Analysis of the underlying medical conditions of fatal cases, based on the observed frequency of the conditions in the general population, confirms the risk for fatal outcome, which is most notably due to immunosuppression, diabetes and respiratory diseases. Our results suggest that early treatment might have had an impact on overall mortality. Identification of risk groups for targeted intervention to prevent fatalities needs to take into account the distribution of underlying conditions in the population.