Objectives To understand how surgical interventions impact the organization and internal integration of the major components of the skull, we address the functional and developmental relationships during perinatal development. Methods A number of methods for quantifying modularity and integration of morphological data are available. Here, measures derived from three-dimensional computed tomographic (CT) images are used to investigate the statistical relationships among measures of the cranial vault, face and cranial base. First, we establish the pattern of associations among quantitative measures in a sample of children unaffected by a craniofacial anomaly. We statistically compare these normative patterns of cranial integration to those of a sample of children with a facial anomaly (complete unilateral complete cleft lip and palate), and to children with a neurocranial anomaly (isolated sagittal synostosis). Finally, we test whether surgery affects the strength and pattern of associations among measures within the cranial base in the affected children. Results Our analyses reveal strong internal integration of the cranial base in unaffected children and in our samples of unoperated cleft lip and palate, and sagittal synostosis. Post-operatively, the magnitude of integration of the cranial base is reduced relative to the pre-operative condition in both samples of children with craniofacial anomalies. Conclusion Our results show how the cranial base adjusts to its broader structural context, and provides added support for the developmental and structural integration of cranial base with both cranial vault and face.