Background: Low socioeconomic status (SES) in childhood is known to be a significant risk factor for mental disorders in Western societies. The purpose of this study was to investigate whether a similar association exists in Japan. Methods. We used data from the World Mental Health Japan Survey conducted from 2002-2006 (weighted N = 1,682). Respondents completed diagnostic interviews that assessed lifetime prevalence of major depression (MD) and generalized anxiety disorder (GAD), as defined by the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition. Associations between parental education (a proxy of SES in childhood) and lifetime onset of both disorders were estimated and stratified by gender using discrete-time survival analysis. Results: Among women, high parental education was positively associated with MD (odds ratio [OR]: 1.81, 95% confidence interval [CI]: 1.03-3.18) in comparison with low parental education, even after adjustment for age, childhood characteristics, and SES in adulthood. This same effect was not found for men. In contrast, higher parental education was associated with GAD (OR: 6.84, 95% CI: 1.62-28.94) in comparison with low parental education among men, but this association was not found among the women, in the fully adjusted model. Conclusions: In Japan, childhood SES is likely to be positively associated with the lifetime onset of mental disorders, regardless of family history of mental disorders, childhood physical illness, or SES in adulthood. Further study is required to replicate the current findings and elucidate the mechanism of the positive association between mental disorders and childhood SES. © 2014 Ochi et al.; licensee BioMed Central Ltd.