Objective: Our study aimed to elucidate the interactive relationship between factors associated with dental caries in school children using decision tree analysis. Research Design: Cross-sectional study Methods: Participants were recruited from public primary schools (9–12 years, 4th to 6th grade) and junior high schools (12–13 years, 1st grade) in Japan. A total of 1775 students (928 boys and 847 girls) were analyzed. Questionnaire survey, oral examination, and saliva test were performed. Multiple logistic regression and decision tree analysis were performed. Results: Multiple logistic regression showed an association between dental caries and toothpaste use, dental attendance and the presence of Streptococcus mutans. Decision tree analysis showed that students with non-regular dental attendance were at a significantly higher risk of dental caries at the late stage of primary school. At the early stage of primary school, high levels of Streptococcus mutans and male sex were factors associated with dental caries. In students with low levels of Streptococcus mutans, using toothpaste occasionally was associated with a high risk of dental caries. Conclusions: In early primary school years, S. mutans may be a useful screening and diagnostic tool for dental caries. In students with high levels of S. mutans, sex may be associated with dental caries. Furthermore, in students with low levels of S. mutans, regular use of toothpaste should be encouraged, and in late primary school years, regular dental attendance should be encouraged to prevent dental caries. Keywords: Dental caries, epidemiology, children, schoolchildren, dental attendance