Abstract Introduction Atherosclerosis is the main cause of mortality in the Czech Republic. In our previous cross-sectional studies, we detected a high prevalence of metabolic cardiovascular risk factors in women before and after menopause and found menopausal transition to be critical period for atherosclerosis acceleration. In the present longitudinal study, we studied changes of main cardiovascular risk factors in women after transition to menopause. Methods We analyzed data of 195 women who became menopausal and 292 women who stayed in menopause during 6-year period. The cardiovascular risk factors under study were as follows: smoking, body mass index, waist circumference, blood pressure, plasma lipids including apolipoprotein B and A1 and fasting glycemia. Results The most striking differences between newly and steadily menopausal women were found in changes of plasma lipids. With the exception of HDL cholesterol all changes were less favorable in newly menopausal women and were not associated with treatment with statins. No significant differences between both groups were found for changes in body mass index, waist circumference, blood pressure and fasting glycemia. Conclusions In longitudinal study we confirmed that time around menopausal transition is one of the most dynamic periods regarding changes of cardiovascular risk factors, mainly plasma lipids.