Background: The socioeconomic and ethnic composition of urban neighbourhoods may affect mortality, but evidence on Central European cities is lacking. The aim of this study was to assess the associations between socioeconomic and ethnic neighbourhood indicators and the mortality of individuals aged 20-64 years old in the two biggest cities of the Slovak Republic. Methods: We obtained data on the characteristics of neighbourhoods and districts (educational level, unemployment, income and share of Roma) and on individual mortality of residents aged 20-64 years old, for the two largest cities in the Slovak Republic (Bratislava and Kosice) in the period 2003-2005. We performed multilevel Poisson regression analyses adjusted for age and gender on the individual (mortality), neighbourhood (education level and share of Roma in population) and district levels (unemployment and income). Results: The proportions of Roma and of low-educated residents were associated with mortality at the neighbourhood level in both cities. Mutually adjusted, only the association with the proportion of Roma remained in the model (risk ratio 1.02; 95 % confidence interval 1.01-1.04). The area indicators - high education, income and unemployment - were not associated with mortality. Conclusion: The proportion of Roma is associated with early mortality in the two biggest cities in the Slovak Republic.