Background: Along with population ageing, limitations in activities of daily living constitute a rising health-related burden in demographically advanced countries. The present study aims to assess the prevalence of self-reported activity limitations derived from chronic conditions and social variation of limitations in the subgroups of the population aged 20–79 years in Estonia. Methods: A cross-sectional study employs data from the second round of the Estonian Family and Fertility Survey, a national project in the framework of Gender and Generation Programme. The target population covers age groups of 20–79 years. A nationally representative probability sample was drawn from the 2000 population census. Face-to-face interviews (n = 7855) were conducted in 2004–05. Results: The estimated prevalence of activity limitations with chronic conditions is 18.5% (95% CI 17.6–19.4) and the prevalence of severe limitations is 10.6% (95% CI 9.9–11.3) among the population. The logistic regression model shows significant differences in activity limitations associated with age, educational attainment and marital status. Conclusions: Judging from our results and the EU structural indicators on health, the prevalence of activity limitations derived from chronic conditions is comparatively high in Estonia. The measures to prevent activity limitations and disability should receive a higher priority in Estonia.