There is growing interest in the influence of socioeconomic status (SES) on health. Individual SES has been shown to be closely related to mortality, morbidity, health-related behavior and access to health care services in Western countries. Whether the same set of social determinants accounts for higher rates of mortality or morbidity in Japan is questionable, because over the past decade the magnitude of the social stratification within the society has increased due to economic and social circumstances. SES must be interpreted within the economic, social, demographic and cultural contexts of a specific country. In this report we discuss the impact of individuals' socioeconomic position on health in Japan with regard to educational attainment, occupational gradient/class, income level, and unemployment. This review is based mainly on papers indexed in Medline/PubMed between 1990 and 2007. We find that socioeconomic differences in mortality, morbidity and risk factors are not uniformly small in Japan. The majority of papers investigate the relationship between education, occupational class and health, but low income and unemployment are not examined sufficiently in Japan. The results also indicate that different socioeconomic contexts and inequality contribute to the mortality, morbidity, and biological and behavioral risk factors in Japan, although the pattern and direction of the relationships may not necessarily be the same in terms of size, pattern, distribution, magnitude and impact as in Western countries. In particular, the association between higher occupational status and lower mortality, as well as higher educational attainment and either mortality or morbidity, is not as strongly expressed among the Japanese. Japan is still one of the healthiest and most egalitarian nations in the world, and social inequalities within the population are less expressed. However, the magnitude of the social stratification has started to increase, and this is an alarming sign.