Abstract Background Vaccination is the key measure available for prevention of the public health burden of annual influenza epidemics. This article describes national trends in seasonal influenza vaccine (IV) coverage in Portugal from 1998/99 to 2010/11, analyzes progress towards meeting WHO 2010 coverage goals, and addresses the effect of major public health threats of the last 12 years (SARS in 2003/04, influenza A (H5N1) in 2005/06, and the influenza A (H1N1)2009 pandemic) on vaccination trends. Methods The National Institute of Health surveyed (12 times) a random sample of Portuguese families. IV coverage was estimated and was adjusted for age distribution and country region. Independence of age and sex coverage distribution was tested using a modified F-statistic with a 5% significance level. The effect of SARS, A (H5N1), and the A (H1N1)2009 pandemic was tested using a meta-regression model. The model was adjusted for IV coverage in the general population and in the age groups. Results Between 1998/99 and 2010/11 IV, coverage in the general population varied between 14.2% (CI 95% : 11.6%–16.8%) and 17.5% (CI 95% : 17.6%–21.6%). There was no trend in coverage (p = 0.097). In the younger age group (