Vaccination is an important public health strategy to prevent adverse health outcomes in the general population and in subjects with chronic diseases. It was the aim of this study to compare data on coverage of recommended vaccinations in men and women with diabetes mellitus and after myocardial infarction (MI) and to analyse trends in three different interview surveys: 1991, 1999 and 2006-07. The data show a rise in influenza vaccination coverage rate in men and women in the general population and in high-risk groups. However, coverage rates in all analysed groups were still strikingly low. Although in soft reported earlier surveys women were vaccinated more often than men, there was a reverse trend observed in the most recent survey. In the survey of 2006-07, men with diabetes or after MI had a higher chance of being vaccinated against influenza when compared to men without these diseases (age adjusted OR: 1.61; 95% CI: 1.29-1.99 and 1.61; 95% CI: 1.21-2.15, respectively). This was, however, not the case in women (OR: 1.10; 95% CI: 0.89-1.35 and 0.87; 95% CI: 0.58-1.33, respectively). Neither men nor women with diabetes mellitus or MI had a significantly higher chance of having pneumococcal vaccination when compared to subjects without these diseases. The observed sex-specific differences demand more research regarding the underlying causes. Strategies to reach higher vaccination coverage in men and women are needed.