The number of children with Metabolic Syndrome (MetS) has recently been increasing in Japan. Few studies have investigated the relationship between MetS and oral health. The aim of this study was to investigate the association between MetS, lifestyle, and oral health status in school children. Our goal is to utilize these results in health education aimed at preventing the onset of MetS in school children and adults. A total of 689 Japanese children (365 boys and 324 girls) aged between 10 and 13 years were examined and waist circumference (WC), ratio of WC to height, blood pressure, fasting blood sugar (FBS), high density lipoprotein-cholesterol, and triglyceride values determined together with oral health status, including dental caries experience (DMFT). The results revealed that 6.5% of the children fell under the health board recognized “MetS or high risk of MetS” (MetS/HR) classification. A total of 140 (20%) children had a high Streptococcus mutans count. The mean WC, FBS, and DMFT values were significantly greater in children with a high salivary S. mutans count (p<0.05). Multiple logistic regression analysis revealed a statistically significance association between MetS/HR, non-breakfast eaters (odds ratio (OR): 2.70), no regular exercise (OR: 2.60), and a high salivary S. mutans count (≥10⁵ CFU/ml; OR: 2.18; p<0.05). The present results indicate that lifestyle and salivary S. mutans count could be useful in screening children for MetS/HR. These variables may be useful in targeting interventions aimed at preventing MetS in school children.