BACKGROUND: Monitoring the time course of socio-economic inequalities in mortality is a key public health issue. The aim of this study is to analyse this trend at an ecological level, in mainland France, over the 1990s, using a deprivation index enabling time comparisons. METHODS: Deprivation indexes (FDep) were built using the 1990 and 1999 data and the same methodology. The indices were defined as the first component of a principal component analysis including four specific socio-economic variables. The time course of the association between mortality and deprivation was evaluated on the 'commune' geographic scale (36 000 U in mainland France), without considering spatial autocorrelation and on the larger 'canton' scale (3700 U), considering spatial autocorrelation. The analysis was carried out by gender, age and degree of urbanicity and applied to general mortality and a specific subcategory: 'avoidable' deaths. RESULTS: Area-level socio-economic inequalities in mortality tended to increase during the 1990s. For the period 1997-2001, the standard mortality ratio (SMR) was 24% higher for the communes in the most deprived quintile than for those in the least deprived quintile, while this differential was of 20% for the period 1988-92. This increase in the differentials concerned especially males and people in the age group of <65 years. For both men and women, it was stronger for the 'avoidable' mortality subcategory. CONCLUSION: As observed at the individual level in previous studies, area-level socio-economic inequalities in health increased during the nineties, while general health improved.