The early modern Edo period in Japan refers to the division of chronological age dated from the seventeenth to nineteenth centuries. During that period, the social structure was stratified, with warriors at the top, followed by farmers, and finally townsmen at the bottom. I aimed to examine carious lesions in deciduous teeth in the commoners from the city of Edo (now Tokyo), to compare them with those in the warriors and commoners from Kyushu, and to reveal differences in the incidence of caries across social classes and regions. I examined 843 deciduous teeth of 115 individuals from the Hitotsubashi site in Tokyo. The comparative samples were obtained from warriors and commoners whose remains were excavated from the Sougenji and Kyoumachi sites, respectively, in Kyushu [Oyamada et al. (2008) Anthropol Sci 116:9-15]. The caries frequency in the Hitotsubashi sample was 11.3 %. Carious lesions in the upper teeth were more frequent than those in the lower teeth in all age groups. The upper incisors exhibited the highest frequency of caries, while there was almost no caries in the lower incisors and canines. I also found population differences in deciduous caries among the Edo populations. Remains of teeth excavated from Hitotsubashi were found to have a mild degree of caries compared to remains of teeth excavated from Sougenji and Kyoumachi in Kyushu in terms of caries frequency and location. Thus, the influence of regional differences in diet and living circumstances was stronger than expected, and the variation observed in the frequency of deciduous caries among the Edo populations cannot be explained by social class alone.