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Background The data on the childhood determinants of adult cardiovascular disease (CVD) are lacking in populations of Eastern Europe that are characterised by substantially high CVD mortality. From a public health perspective, it is important to identify high-risk individuals as early as possible in order to have the greatest benefit of preventive interventions. The aim of this study was to evaluate the associations of childhood and adulthood traditional risk factors with subclinical atherosclerosis and arterial stiffness in a Lithuanian cohort followed up for 35 years. Methods The study cohort consisted of 380 adults aged 48–49 from Kaunas Cardiovascular Risk Cohort study, who were followed up since childhood (12–13 years). The baseline survey (1977) included blood pressure (BP) and anthropometric measurements and sexual maturity scale. In the follow-up survey (2012), BP, anthropometric and lipids measurements, interview about smoking, measurement of carotid intima-media thickness (IMT) and determination of pulse wave velocity (PWV) were performed. Two types of general linear models were applied to test the associations of childhood and adulthood risk factors with IMT and PWV. Model 1 included only childhood variables. In model 2, adulthood variables were added to childhood variables. Results In linear regression model with childhood variables childhood systolic BP (β = 0.014; p = 0.016) and BMI (β = 0.006; p = 0.003) were directly associated with IMT only in women. When adulthood variables were included into regression model, the association between childhood systolic BP and IMT remained significant (β = 0.013; p = 0.021), while childhood BMI was not associated with IMT (β = 0.003; p = 0.143). Additionally, association of adult smoking and IMT was found in women (β = 0.033; p = 0.018). IMT of men was directly related to adult systolic BP (β = 0.022; p = 0.018) and inversely to HDL cholesterol level (β = −0.044; p = 0.021). PWV was directly associated only with adult systolic BP in both genders (β = 0.729 for men and β = 0.476 for women; p = 0.001). Conclusions Sex differences in the associations between childhood and adulthood risk factors and subclinical atherosclerosis were found. The results of the study support efforts to reduce conventional risk factors both in childhood and adulthood for the primary prevention of atherosclerosis.