OBJECTIVE: The people of the Yayoi period (5th C b.c.-3rd C a.d.), who were the first wet-rice agriculturalists in ancient Japan, had carious lesions that were most frequently located on the root surfaces of their teeth. Root surface exposure is a prerequisite for this type of decay, and alveolar bone loss is the main cause of such exposure. Therefore, we identify the factors associated with root caries, and examine the relationship between root caries and alveolar bone loss in the people of the Yayoi period. MATERIALS AND METHODS: This study was performed using 263 sets of ancient skeletal remains that are believed to be from the Yayoi period and that were excavated at 49 archaeological sites in western Japan. Using 5010 teeth found among the remains, we analysed the relationship between the prevalence of root caries and the cemento-enamel junction-alveolar crest (CEJ-AC) distance. RESULTS: The prevalence of root caries and the mean number of teeth with root caries per person were significantly correlated with age, the presence of coronal caries and the mean CEJ-AC distance per person. We also found that as the mean CEJ-AC distance per tooth surface increased, the percentage of the root surface affected by caries increased. Moreover, after excluding the lingual (palatal) side, the mean CEJ-AC distance per surface was significantly greater for those tooth surfaces with root caries. CONCLUSION: We present the first evidence that the occurrence of root caries correlated with the CEJ-AC distance in the Yayoi people of Japan.