Aim To determine biological (sex and age), socioeconomic (marital status, education, and mother tongue) and geographical (region) factors connected with causes of death and lifespan (age at death, years-of-potential-life-lost, and mortality rate) in Slovenia in the 1990s. Methods In this population-based cross-sectional study, we analyzed all deaths in the 25-64 age group (N = 14 816) in Slovenia in 1992, 1995, and 1998. Causes of death, classified into groups according to the 10th revision of International Classification of Diseases, were linked to the data on the deceased from the 1991 Census. Stratified contingency-table analyses were performed. Years-of-potential-life-lost (YPLL) were calculated on the basis of population life-tables stratified by region and linearly modeled by the characteristics of the deceased. Poisson regression was applied to test the differences in mortality rate. Results Across all socioeconomic strata, men died at younger age than women (index of excess mortality in men exceeded 200 for all studied years) and from different prevailing causes (injuries in men aged <45 years; neoplasms in women aged >35 years). For men, higher education was associated with fewer deaths from digestive and respiratory system diseases. The least educated women died relatively often from circulatory diseases, but rarely from neoplasms. Single people died from neoplasms less often. Marriage in comparison with divorce reduced the mortality rate by 1.9-fold in both men and women (P<0.001). Mortality rate in both men and women decreased with increasing education level (P<0.001). Mortality rate of ethnic Slovenians was half the mortality rate of ethnic minority members and immigrants (P<0.001). Analysis of YPLL revealed limited and nonlinear impact of education level on premature mortality. The share of neoplasms was the highest in the cluster of socioeconomically prosperous regions, whereas the share of circulatory diseases was increased in poorer regions. Significant differences were found between individual regions in age at death and mortality rate, and the differences decreased over the studied period. Conclusion These data may aid in understanding the nature, prevalence and consequences of mortality as related to socioeconomic inequalities, and thus serve as a basis for setting health and social policy goals and planning health measures.