Study objective: This study examined the change in ethnic differences in mortality in Estonia 1989–2000. Design: Two unlinked cross sectional census based analyses were compared. Total and cause specific mortality was analysed for ethnic Estonians and Russians. The absolute differences in mortality were evaluated through life expectancy at birth and age standardised mortality rates. Relative differences were assessed by mortality rate ratios with 95% confidence intervals, calculated using Poisson regression. Setting: Estonia before and after the fall of the Soviet Union. Participants: Individual cause specific death data for 1987–1990 (69 549 deaths) and for 1999–2000 (33 809 deaths) came from the national mortality database. Population denominators came from the population censuses of 1989 and 2000. Main results: In the period 1989–2000, ethnic differences in life expectancy increased from 0.4 years to 6.1 years among men and from 0.6 years to 3.5 years among women. In 2000, Russians had a higher mortality than Estonians in all age groups and for almost all selected causes of death. The largest differences were found for some alcohol related causes of death especially in 2000. Conclusions: Political and economic upheaval, increasing poverty, and alcohol consumption can be considered the main underlying causes of the widening ethnic mortality gap.