ABSTRACT: BACKGROUND: Estonian and Russian ethnic groups in Estonia differ from one another in several aspects, such as historic and socio-economic background, language and culture. The aim of the current study was to examine ethnic differences in cancer incidence in Estonia, and to compare the situation before and after the profound political and economical changes in the early 1990s. METHODS: Two cross-sectional unlinked census-based cancer incidence analyses were performed. Cancer incidence data were obtained from the Estonian Cancer Registry. Population denominators came from the population censuses of 1989 and 2000. Standardized cancer incidence rates were calculated for men and women for the aggregate periods 1988-1990 and 1999-2000. Differences in cancer incidence between Estonians and Russians in 1989 and 2000 were estimated for both sexes, using standardized rate ratios with 95% confidence intervals. RESULTS: In 1988-1990, the total cancer incidence in Russian men was higher than that in Estonian men (SRR = 1.26, 95%CI = 1.19-1.34). In 1999-2000, the total cancer incidence in men showed only slightly higher estimates in Russians than in Estonians (SRR = 1.06, 95%CI = 0.99-1.32). Cancers of stomach, colon and lung had persisting higher values in Russian men in 1999-2000. In women, the differences were smaller than in men, and the total cancer incidence showed no differences relating to neither of the time periods studied. With regard to specific sites, excess of stomach cancer incidence was seen in Russian women (SRR = 1.45, 95%CI = 1.15-1.81). The ethnic differences in general decreased between the two time periods studied. CONCLUSION: Some of the differences in cancer rates between the Estonians and Russians in Estonia are likely to be attributable to the variation in exposure to specific etiologic factors that are causedby differences in lifestyle and habits, such as hygiene, smoking and drinking. Further research with a view to understanding these ethnic differences in cancer incidence is warranted.