The extent that risk factors, identified in Western countries, account for health inequalities in Japan remains unclear. We analysed a nationally representative sample (Comprehensive Survey of Living Conditions surveyed in 2001 (n = 40,243)). The cross-sectional association between self-rated fair or poor health and household income and a theory-based occupational social class was summarised using the relative index of inequality [RII]. The percentage attenuation in RII accounted for by candidate contributory factors - material, psychosocial, social relational and behavioural - was computed. The results showed that the RII for household income based on self-rated fair or poor health was reduced after including the four candidate contributory factors in the model by 20% (95% CI 2.1, 43.6) and 44% (95% CI 18.2, 92.5) in men and women, respectively. The RII for the Japanese Socioeconomic Classification [J-SEC] was reduced, not significantly, by 22% (95% CI -6.3, 100.0) in men in the corresponding model, while J-SEC was not associated with self-rated health in women. Material factors produced the most consistent and strong attenuation in RII for both socioeconomic indicators, while the contributions attributable to behaviour alone were modest. Social relational factors consistently attenuated the RII for both socioeconomic indicators in men whereas they did not make an independent contribution in women. The influence of perceived stress was inconsistent and depended on the socioeconomic indicator used. In summary, social inequalities in self-rated fair or poor health were reduced to a degree by the factors included. The results indicate that the levelling of health across the socioeconomic hierarchy needs to consider a wide range of factors, including material and psychosocial factors, in addition to the behavioural factors upon which the current public health policies in Japan focus. The analyses in this study need to be replicated using a longitudinal study design to confirm the roles of different factors in health inequalities. Copyright © 2014 Elsevier Ltd. All rights reserved.