BackgroundSeasonal influenza is one of the most significant infectious diseases in Germany; epidemic outbreaks occur every winter and cause substantial morbidity and mortality. However, published data from Germany on the current economic burden of influenza and the costs per episode are lacking.MethodsA retrospective database analysis was conducted using a longitudinal electronic medical records database (IMS Disease Analyzer). Patients with influenza, diagnosed by German office-based physicians using ICD-10 J09-11 (International Classification of Diseases, 10th revision), who were observable in the database from 12 months before the index (diagnosis) date until 1 month afterwards, were included. The selection window, defined to cover two influenza seasons, was May 2010 to April 2012. Direct and indirect costs were evaluated from payer, patient and societal perspectives. Published unit costs and tariffs from Germany (2012) were used for the analysis.ResultsA total of 21,039 influenza-attributable episodes in 17,836 adults, managed by primary care physicians (PCP) and 7,107 episodes in 6,288 children, managed by pediatricians, were eligible for analysis. The mean (±Standard Deviation (SD)) age of the adults with at least one episode was 46 (±18) years and 7 (±4) years in the children. The presence of clinical risk factors was documented for 39 % episodes in adults and 24 % episodes in children, with the most common being cardiovascular diseases in adults (29 %) and chronic respiratory diseases in children (23 %). Complications and severe symptoms accompanied the influenza-attributable episode (adults: 37 %, children: 54 %), bronchitis (adults: 16 %, children: 19 %) and acute upper respiratory infection (adults: 15 %, children: 21 %) being the most frequent. From a societal perspective, the total average mean cost (±SD) per episode was €514 (±609) in adults, where work days lost were the main cost driver (82 %), and €105 (±224) in children. Complications and severe symptoms increased the cost per episode versus episodes without by 1.7 times in adults (€684 (±713) vs. €413 (±510)) and nearly 3 times in children (€149 (±278) vs. €55 (±116)).ConclusionsBased on a large patient sample derived from representative PCP and pediatricians panels, our results demonstrate that seasonal influenza is associated with substantial clinical and economic burden in Germany.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-015-1885-0) contains supplementary material, which is available to authorized users.