Background: Stage at diagnosis is one of the most important predictors of breast cancer survival. The objective of this population-based study was to examine the impact of age, period of diagnosis and place of residence on breast cancer stage at diagnosis in Estonia. Methods: Female breast cancer cases reported to the Estonian Cancer Registry in 1995–2006 with a known extent of disease were included. Logistic regression was used to estimate the risk of advanced stage (non-localized) disease. Results: Overall, 56% of the 6936 women included in the analysis were diagnosed at advanced stage. The risk of advanced disease at diagnosis decreased over the study period in all age groups, but the change was much larger among women aged 50–69 years than among women in younger and older age groups. Multivariate analysis indicated that the strongest predictor of advanced stage disease was the place of residence. Compared with Tallinn (the capital of Estonia), living in Tartu (a small town with a university hospital) was associated with a significant 36% reduction in risk while the odds ratio associated with living in a marginal industrial county (Ida-Viru) was 1.52 (95% confidence interval 1.29–1.79). Conclusions: The observed regional variations are most likely due to differences in education, unemployment and health care access. Younger and elderly women, those living in remote areas and of lower socio-economic status should be addressed with specific measures to promote earlier detection of breast cancer, particularly in view of current economic difficulties and a sharply rising unemployment rate.