Background Prices of alcohol and income tend to influence how much people buy and consume alcohol. Price and income may be combined into one measure, affordability of alcohol. Research on the association between affordability of alcohol and alcohol-related harm is scarce. Furthermore, no research exists on how this association varies across different subpopulations. We estimated the effects of affordability of alcohol on alcohol-related mortality according to gender and education in Finland and Sweden. Methods Vector-autoregressive time series modelling was applied to the quarter-annual aggregations of alcohol-related deaths and affordability of alcohol in Finland in 1988-2007 and in Sweden in 1991-2008. Alcohol-related mortality was defined using information on both underlying and contributory causes of death. We calculated affordability of alcohol index using information on personal taxable income and prices of various types of alcohol. Results Among Finnish men with secondary education, an increase of 1% in the affordability of total alcohol was associated with an increase of 0.028% (95% CI 0.004 to 0.053) in alcohol-related mortality. Similar associations were also found for affordability for various types of alcohol and for beer only in the lowest education group. We found few other significant positive associations for other subpopulations in Finland or Sweden. However, reverse associations were found among secondary-educated Swedish women. Conclusions Overall, the associations between affordability of alcohol and alcohol-related mortality were relatively weak. Increased affordability of total alcoholic beverages was associated with higher rates of alcohol-related mortality only among Finnish men with secondary education.