Introduction: Chondrocranial-derived components of the craniofacial skeleton are thought to exert a morphogenetic influence on surrounding intramembranous-derived skeletal structures. In our previous study (Foster and Holton, 2016), we found that the ontogenetic relationship between the nasal septum (derived primarily from the chondrocranium) and surrounding intramembranous-derived facial skeleton was highly variable in BL6 and C3H mice. The purpose of our present study was to examine samples of BL6 and C3H mice from 3 to 15 weeks of age to determine whether the variable interaction noted previously extends to chondrocranial- and intramembranous-derived components throughout the cranium. Methods: Cross-sectional samples of male C57BL/6J (BL6) and C3H/HeJ (C3H) at 3 (n=18) and 15 (n=30) weeks of age were studied. All mouse crania were scanned using a Skyscan 1272 microCT scanner, and a series of three-dimensional traditional and semilandmark coordinate landmarks were collected. Geometric morphometric techniques were utilized for data analysis. Results: During the period of 3-15 weeks of age, there was considerable variation in the ontogeny of chondrocranial- and intramembranous-derived craniofacial regions. Conclusions: During the period of 3-15 weeks of age, C3H mice were characterized by a relative enlargement of the chondrocranial-derived craniofacial skeleton. The chondrocranial morphology of the C3H mice may be a causal factor in the increased magnitude of variation seen in the C3H intramembranous-derived facial skeleton. Developmental variation within specific components of the craniofacial complex may account for taxonomic variation in facial height that accompanies anteroposterior facial skeletal reduction characteristic of taxa such as anthropoid primates.