Health disparities in Japan are attracting increasing attention. Temporal trends in health disparities should be continuously monitored using multiple indices of socioeconomic status (SES) and health-related outcomes. We explored changes in socioeconomic differences in the health of Japanese adults during 2000–2010. The data was taken from the Japanese General Social Surveys, the cross-sectional surveys for nationally representative samples of Japanese adults. We used 14,193 samples (individuals of 20–64 years of age) in our analysis. We estimated age-adjusted prevalence ratios of the lowest SES group in comparison with the highest SES group using Poisson regression models with robust error variance. Relative index of inequality (RII) and slope index of inequality (SII) were also calculated. We examined the changes in the association between health-related outcomes (self-rated health (SRH), smoking, and physical activity) and SES indices (income, education, occupation, and subjective social class identification). The results showed temporally expanding trends for the associations of current smoking with SES, especially among women, in both relative and absolute measures. In contrast, no expanding trends were seen for SRH and physical activity. Although the smoking rates declined through the first decade of the 21st century, the socioeconomic disparities in smoking prevalence among Japanese adults expanded, especially among women. Researchers and policymakers should continuously monitor the trends that may cause future disparities in smoking-related morbidity and mortality. Keywords: Japan, Socioeconomic disparity, Temporal trends, Smoking, Self-rated health