SUMMARY The generation of coordinated morphological change over time results from the interconnectedness of evolution and development. The modular architecture of development results in varying degrees of integration and independence among parts of the phenotype, and facilitates the production of phenotypic variation in complex anatomical units composed of multiple tissue types. Here we use geometric morphometrics to investigate modularity in the arterial Circle of Willis (CW) and skull of the CD-1 laboratory mouse. We contrast a hypothesis of tight integration between these tissues with a hypothesis of more modular organization, to determine the level at which natural selection works to generate coordinated change. We report a complex pattern of covariation that indicates that the skull and CW are highly integrated and developmentally linked. Further, we report higher levels of fluctuating asymmetry in the CW than in the skull, suggesting a greater potential for lability in this tissue. These results suggest that epigenetic interactions or genetic influences on regional development are more important determinants of covariation structure than the factors that produce covariation within individual tissues or organ systems.