Objective The aim of this study is to clarify the association between area-based social capital and suicide rate among municipalities of Tokyo. Methods The study areas were 20 administrative municipalities of Tokyo. Social capital (i.e., organizational membership, social trust, fairness, helpfulness, and confidence in organizations) was measured based on data from a previous survey (response rate 28 %). Gender-specific ageadjusted suicide rates averaged over 5 years, sociodemographic, and other area characteristics were obtained from relevant national statistics. Multiple linear regression analysis of suicide rates was applied on each social capital variable, adjusting for the other area characteristics. Results There was no significant crude Pearson's correlation between any social capital variable and suicide rate. Multiple regression analyses revealed a significant negative association between social trust and suicide rate for men (p = 0.04). Conclusions While based on only limited evidence from a cross-sectional ecological study, area-based social trust may be associated with decreased suicide rates for men in Tokyo.