The early modern Edo period in Japan denotes a chronological division between the AD 17th and 19th centuries when social structure was stratified. This study aimed to examine the occurrence of dental caries in the deciduous teeth of commoner children in Sakai City (Osaka, Japan), comparing them with those excavated in other regions, eventually clarifying variations in prevalence of deciduous caries and the causative factors contributing to such variations. Results indicated a biased distribution pattern in caries prevalence. Caries were frequently present in maxillary incisors while few occurrences in the mandibular counterparts were observed. Another important finding was the population‐level differences in caries prevalence – the Sakai sample displayed systematically lower frequencies of caries than warriors and commoners from Kyushu in western Japan; thus, causative factors can be hypothesized to be not only social classes but also regional differences in living conditions. These findings proved the presence of intra‐ and inter‐population variation in deciduous caries based on children's skeletons from socially stratified societies in different geographical regions, and demonstrated that deciduous caries provide bioarchaeologists with information on population diversity apparent in caries prevalence and cariogenic diets.