Aims: To explore inequalities in total mortality between small areas of 16 European cities for men and women, as well as to analyse the relationship between these geographical inequalities and their socioeconomic indicators. Methods: A cross-sectional ecological design was used to analyse small areas in 16 European cities (26,229,104 inhabitants). Most cities had mortality data for a period between 2000 and 2008 and population size data for the same period. Socioeconomic indicators included an index of socioeconomic deprivation, unemployment, and educational level. We estimated standardised mortality ratios and controlled for their variability using Bayesian models. We estimated relative risk of mortality and excess number of deaths according to socioeconomic indicators. Results: We observed a consistent pattern of inequality in mortality in almost all cities, with mortality increasing in parallel with socioeconomic deprivation. Socioeconomic inequalities in mortality were more pronounced for men than women, and relative inequalities were greater in Eastern and Northern European cities, and lower in some Western (men) and Southern (women) European cities. The pattern of excess number of deaths was slightly different, with greater inequality in some Western and Northern European cities and also in Budapest, and lower among women in Madrid and Barcelona. Conclusions: In this study, we report a consistent pattern of socioeconomic inequalities in mortality in 16 European cities. Future studies should further explore specific causes of death, in order to determine whether the general pattern observed is consistent for each cause of death.