Knowledge of the pattern of human craniofacial development in the fetal period is important for understanding the mechanisms underlying the emergence of variations in human craniofacial morphology. However, the precise character of the prenatal ontogenetic development of the human cranium has yet to be fully established. This study investigates ontogenetic changes in cranial shape in the fetal period, as exhibited in Japanese fetal specimens housed at Kyoto University. A total of 31 human fetal specimens aged from approximately 8 to 42 weeks of gestation underwent helical computed tomographic scanning, and 68 landmarks were digitized on the internal and external surfaces of the extracted crania. Ontogenetic shape change was then analyzed cross-sectionally and three-dimensionally using a geometric morphometric technique. The results of the present study are generally consistent with previously reported findings. It was found that during the prenatal ontogenetic process, the growth rate of the length of the cranium is greater than that of the width and height, and the growth rate of the length of the posterior cranial base is smaller than that of the anterior cranial base. Furthermore, it was observed that the change in shape of the human viscerocranium is smaller than that of the neurocranium during the fetal period, and that concurrently the basicranium extends by approximately 8° due to the relative elevation of the basilar and lateral parts of occipital bone. These specific growth-related changes are the opposite of those reported for the postnatal period. Our findings therefore indicate that the allometric pattern of the human cranium is not a simple continuous transformation, but changes drastically from before to after birth.