To track the trends in general health indicators and the prevalence of cardiovascular diseases (CVD), high blood pressure and elevated blood cholesterol in the middle-aged urban population in the Czech Republic in 1998–2010.Cross-sectional study.The following data from the three-phase HELEN (HEalth – Lifestyle – ENvironment) study, a prevalence questionnaire survey, were analysed: data collected from 8214 subjects in phase I, 6107 subjects in phase II, and 4389 subjects in phase III. The study subjects were aged 45–54 years and the study period spanned from 1998 to 2010. The differences in the indicators between phases were evaluated by binary and ordinal logistic regression models at a significance level of 0.01.Over the study period, a significant increase was observed in the proportion of respondents who self-rated their health as very good or good: from 46.6% to 51.0% in males (P = 0.006) and from 45.5% to 49.9% in females (P < 0.001). At the same time, the rates of respondents under long-term medical follow-up rose significantly from 36.3% to 44.3% (P < 0.001) and from 46.4% to 56.2% (P < 0.001), respectively.CVD prevalence did not change although the percentage of males and females with high blood pressure (from 29.3% to 36.6% and from 26.0% to 31.2%, respectively) and elevated total cholesterol (from 29.0% to 36.6% and from 27.3% to 32.4%, respectively) increased significantly.Self-rated health among the middle-aged population in the Czech Republic improved during the 1998–2010 period, but, at the same time, more people needed to be followed up for a disease. The proportions of respondents with hypertension and elevated blood cholesterol increased while the CVD rates did not vary significantly.