Objectives: A few studies have revealed the impact of neighborhood social capital on oral health among young people. We sought to examine the associations of social capital in three settings (families, neighborhoods, and schools) with self-rated oral health among a sample of college students in Japan. Methods: Cross-sectional survey of 967 students in Okayama University, aged 18 and 19 years, was carried out. Logistic regression was used to examine the associations of poor self-rated oral health with perceptions of social capital, adjusting for self-perceived household income category and oral health behaviors. Results: The prevalence of subjects with poor self-rated oral health was 22%. Adjusted for gender, self-perceived household income category, dental fear, toothbrush frequency, and dental floss use, poor self-rated oral health was significantly associated with lower level of neighborhood trust [odds ratio (OR) 2.22; 95% confidence interval (CI): 1.40-3.54] and lower level of vertical trust in school (OR 1.71; 95% CI: 1.05-2.80). Low informal social control was unexpectedly associated with better oral health (OR 0.54; 95% CI: 0.34-0.85). Conclusion: The association of social capital with self-rated oral health is not uniform. Higher trust is associated with better oral health, whereas higher informal control in the community is associated with worse oral health.