Background A 9.5-year follow-up of the Kaunas-Rotterdam Intervention Study (KRIS) provided an opportunity to compare mortality patterns and rates in a population from Lithuania, one of the former republics of the Soviet Union, with a population from the Netherlands. These populations consisted of 2452 and 3365 males, respectively, aged 45-60 years. In 1972-1974, these males were extensively screened for cardiovascular risk factors, using uniform methods. Methods and results During the follow-up, 303 males in Kaunas (Lithuania) and 350 males in Rotterdam (the Netherlands) died. Using Cox proportional hazards and logistic regression analysis, it was found that all-cause mortality rates during follow-up were 30% higher in Kaunas; this was mainly due to higher mortality rates from external causes (relative risk = 6.69), stomach cancer (RR = 2.78), stroke (RR = 2.30) and infectious diseases (RR = 12.43). The risk of fatal and non-fatal coronary heart disease (CHD) was, however, smaller in Kaunas (RR = 0.72). This lower risk closely corresponded with the Lithuanian risk profile which could be described by less smoking, lower cholesterol levels, and higher physical activity. As Lithuanians had a more advantageous cardiovascular risk profile, the higher Lithuanian all-cause mortality rates could not be explained by this risk profile. Conclusions The results provide evidence for geographical differences in mortality and morbidity between Lithuania and the Netherlands. Population-specific health behaviours were shown to be involved in differences in the risk of CHD. The lower CHD rates in Eastern European communities in the 1970s, in this study confirmed for Lithuania, suggests that the apex of the CHD epidemic had not yet reached the Lithuanian population.