In Austria, a country with a total population of approximately 8.3 million, the published estimates of influenza-associated deaths within the past decade are surprisingly high (up to 6000 deaths per year) when compared to neighbouring countries. The objective of our analysis was to provide reliable estimates of the annual influenza-related deaths in Austria. We estimated the seasonal influenza-related excess mortality by calculating the difference between all-cause mortality observed during the influenza season and the baseline values to be expected during that time span if increased influenza activity was absent. Increased influenza activity was defined as moderate, usual or high, categorized by the influenza activity index using weekly data from the Austrian sentinel clinical surveillance system. For obtaining estimates of baseline all-cause mortality, a cyclic regression model was applied to the time series data on weekly all-cause mortality from 2001 to 2009. Austrian seasonal influenza-related excess mortality peaked in the seasons 2002/2003 (1060 excess deaths), 2004/2005 (1102 excess deaths) and 2008/2009 (1192 excess deaths). The rising trend observed is in parallel with the increasing proportion of the Austrian population older than 65 years for the same time span (2001:15.5%; 2009: 17.5%). Our findings on seasonal influenza-related excess mortality are in accordance with the estimates from Germany and Switzerland, which were derived from a similar approach. In order to gain and to preserve higher compliance with influenza vaccination initiatives, it is essential to have reliable data on influenza-related mortality. Thus, the numbers presented so far by Austrian public health institutions must be challenged.