This study aimed to reveal the causal relationships of dietary and lifestyle habits with socio-economic status (SES) and three health-related factors (physical, mental and social health) in elderly urban dwellers in Japan. All the elderly urban dwellers aged 65 years or more in an urban area of Tokyo were surveyed using a self-administered questionnaire in September 2001. There were 13,195 respondents with a response rate of 80.2%. And then, two follow-up surveys were conducted in 2004 and 2007, respectively. Finally, 8162 respondents were included as analysis subjects. Data analysis was performed using factor analysis and structural equation modelling (SEM). As a result of an exploratory factor analysis, three latent variables ('dietary and lifestyle habits in 2004', 'SES in 2001' and 'three health-related factors in 2001') were defined and applied in the SEM. From the best-fit models, dietary and lifestyle habits in 2004 were well explained by SES and three health-related factors in 2001 (R2 1/4 0.44 for elderly men and R2 1/4 0.61 for elderly women). The results showed that dietary and lifestyle habits in 2004 were not only directly affected by SES and the three health-related factors in 2001, but also indirectly by SES via the three health-related factors. Moreover, the causal relationships between the three latent variables depended on sex and age. In conclusion, SES as a basic determinant enough income, high education level and good physical, mental and social health favoured both directly and indirectly the practice of healthy or desirable lifestyle habits of the elderly late in life. It will be necessary to construct a model with higher external validity in a future study. © 2012 The Institute of Urban Sciences.