Deciduous tooth crown measurements were investigated among the inhabitants of the Japanese islands over the past 4000 years. Mesiodistal and buccolingual crown diameters were measured in Neolithic Jomon, Aeneolithic Yayoi (divided into the samples from Tanegashima island and from other western Japanese sites), protohistoric Kofun, medieval, early modern Edo, modern Japanese and early modern Sakhalin Ainu samples. Overall deciduous tooth size decreased in the order of Tanegashima Yayoi, Yayoi, Jomon, Kofun, Edo, modern, medieval, and Sakhalin Ainu samples. The deciduous tooth size of the Jomon sample was larger than that of the modern Japanese, opposite to the relationship in their permanent dentition found by Brace and Nagai (1982). Diachronic size change of the Yayoi and post-Yayoi Japanese deciduous teeth was similar to that of their permanent teeth disclosed by Matsumura (1994). There was no apparent distinction between the Jomon and Yayoi samples, both in overall tooth size and in the proportion of tooth size. The Jomon and Tanegashima Yayoi samples had relatively larger deciduous teeth than the Yayoi and post-Yayoi Japanese samples when compared with their permanent teeth. It is likely that there was a difference in dental developmental pattern between the two groups.