Characteristics of the modern Japanese show a concentric circular geographic distribution: the people in central Japan around the Kinki District are morphologically different from those in peripheral Japan around the Tohoku District and the Kyushu District. In 1983 and 1986, Kouchi thought that the concentric distribution might have appeared between the late Edo period (the 18th to the early 19th century) and the modern period (the early 20th century). The purpose of the present study is to examine the morphological secular changes in Japanese crania from the late Edo period to the modern period and to clarify the formation of the concentric distribution of the cranial morphology. The results is that, first, the tendencies of the secular changes from the late Edo period to the modern period are similar in all regions. Second, the inter-regional differences of craniofacial characteristics have been becoming smaller from the late Edo period to the modern period. Such changes have also been found among the secular changes from the early to the late 20th century. Therefore, it is considered that the secular changes between the late Edo period and the modern period continue to the present day. Next, the present study shows that a concentric distribution of morphological characteristics existed in the late Edo period, and continues to exist in the modern period. Thus, it is possible that the concentric distribution of morphological characteristics of the modern Japanese was formed before the late Edo period, and that the secular changes between the Edo period and the modern period did not influence the formation of the observed concentric distribution. The concentric distribution might have appeared between the prehistoric Jomon period (before the third century B.C.) and the Edo period, because such a concentric distribution has never been demonstrated based on the materials from the Jomon period. Although the reasons for the concentric distribution are not fully understood, both the influx of immigrants from the Asian Continent during the Yayoi period (the third century B.C. to the third century A.D.) and the environmental events occurring between the Kofun period (the third to the seventh century A.D.) and the Edo period could be possible influences.