Previous research has highlighted the role of self-rated health (SRH) as an important predictor of mortality. With substantial ethnic differences in SRH and mortality reported in Estonia, this study aims to examine the ethnic variation in SRH–mortality association in this setting. Materials and methods The baseline data come from nationally representative 1996 Estonian Health Interview Survey. Individual records of 3983 respondents in the 25–79 age group were linked with mortality data with 17 years follow-up time. The association between SRH and all-cause mortality was analysed using the Cox regression for two ethnic groups and separately for men and women. Results Among ethnic Estonians, both men and women with bad or very bad SRH had about 60% higher mortality compared to those with good or very good SRH even after adjustment for age, socioeconomic and health-related variables. In contrast, SRH did not predict mortality among non-Estonian men and women. A strong and universal inverse association with mortality was found for personal income. Education (among men) and occupation (among women) predicted mortality only among non-Estonians, whereas ever smoking was associated with mortality in Estonian men and women. Overweight women had lower mortality risk compared to women in normal weight category. Conclusions We found considerable ethnic variation in SRH–mortality association and in socioeconomic predictors of mortality. Further research, preferably focusing on cause-specific mortality and reporting heterogeneity of SRH could potentially shed further light on ethnic differences in SRH–mortality association in Estonia and more generally on socioeconomic inequalities in mortality in Eastern Europe.