Congenital anomalies of the brain frequently correspond to cranial base anomalies, and a detailed description of morphology and individual variations in the developing cranial base is of clinical importance for diagnosing anomalies. Development of the human cranial base has been studied using dissection, computed tomography, and magnetic resonance imaging, each of which has advantages and disadvantages. We here examined development of the normal human fetal cranial base using bone staining, which allows for direct observation of the ossification centers and precise three-dimensional measurements. We observed alizarin red S-stained sphenoids and basiocciputs of 22 normal formalin-fixed human fetuses with crown-rump lengths (CRL) of 115-175 mm. We defined landmarks and measured sphenoids and basiocciputs using a fine caliper. Growth patterns of these ossifying bones were obtained, and we found similarities and differences among the growth patterns. We also observed individual variations in the ossification patterns, in particular, single-or double-ossification center patterns for the basisphenoid. The orbitosphenoid and basisphenoid widths and ratios of the widths to the total cranial base width were significantly different between the two pattern groups, whereas the other measurements and their ratios to the total cranial base did not differ between the groups. We measured the cerebrum and pons in different sets of 22 human fetuses with CRLs of 105-186 mm and found close relationships with the development of corresponding parts of the cranial base. The results contribute to the quantitative and qualitative information about the growth patterns and variations during human fetal cranial base development.