Background: A recent study from Japan suggested that geographic inequalities in all-cause premature adult mortality have increased since 1995 in both sexes even after adjusting for individual age and occupation in 47 prefectures. Such variations can arise from compositional effects as well as contextual effects. In this study, we sought to further examine the emerging geographic inequalities in all-cause mortality, by exploring the relative contribution of composition and context in each prefecture.Methods: We used the 2005 vital statistics and census data among those aged 25 or older. The total number of decedents was 524,785 men and 455,863 women. We estimated gender-specific two-level logistic regression to model mortality risk as a function of age, occupation, and residence in 47 prefectures. Prefecture-level variance was used as an estimate of geographic inequalities in mortality, and prefectures were ranked by odds ratios (ORs), with the reference being the grand mean of all prefectures (value = 1).Results: Overall, the degree of geographic inequalities was more pronounced when we did not account for the composition (i.e., age and occupation) in each prefecture. Even after adjusting for the composition, however, substantial differences remained in mortality risk across prefectures with ORs ranging from 0.870 (Okinawa) to 1.190 (Aomori) for men and from 0.864 (Shimane) to 1.132 (Aichi) for women. In some prefectures (e. g., Aomori), adjustment for composition showed little change in ORs, while we observed substantial attenuation in ORs in other prefectures (e. g., Akita). We also observed qualitative changes in some prefectures (e. g., Tokyo). No clear associations were observed between prefecture-level socioeconomic status variables and the risk of mortality in either sex.Conclusions: Geographic disparities in mortality across prefectures are quite substantial and cannot be fully explained by differences in population composition. The relative contribution of composition and context to health inequalities considerably vary across prefectures.