The erosion of social capital in more unequal societies is one mechanism for the association between income inequality and health. However, there are relatively few multi-level studies on the relation between income inequality, social capital and health outcomes. Existing studies have not used different types of health outcomes, such as dental status, a life-course measure of dental disease reflecting physical function in older adults, and self-rated health, which reflects current health status. The objective of this study was to assess whether individual and community social capital attenuated the associations between income inequality and two disparate health outcomes, self-rated health and dental status in Japan. Self-administered questionnaires were mailed to subjects in an ongoing Japanese prospective cohort study, the Aichi Gerontological Evaluation Study Project in 2003. Responses in Aichi, Japan, obtained from 5715 subjects and 3451 were included in the final analysis. The Gini coefficient was used as a measure of income inequality. Trust and volunteering were used as cognitive and structural individual-level social capital measures. Rates of subjects reporting mistrust and non-volunteering in each local district were used as cognitive and structural community-level social capital variables respectively. The covariates were sex, age, marital status, education, individual- and community-level equivalent income and smoking status. Dichotomized responses of self-rated health and number of remaining teeth were used as outcomes in multi-level logistic regression models. Income inequality was significantly associated with poor dental status and marginally significantly associated with poor self-rated health. Community-level structural social capital attenuated the covariate-adjusted odds ratio of income inequality for self-rated health by 16% whereas the association between income inequality and dental status was not substantially changed by any social capital variables. Social capital partially accounted for the association between income inequality and self-rated health but did not affect the strong association of income inequality and dental status.