The different forms of morphological integration, developmental, functional, genetic, and evolutionary are defined and their theoretical relationships explored. Quantitative genetic models predict that the co-selection of traits involved in a common function will lead to pleiotropic effects at the loci affecting them while functionally-unrelated traits will be affected by separate sets of loci (Wagner, 1996). The patterns of genetic variation produced by these pleiotropic mutations and stabilizing selection for functionally and developmentally interacting traits results in their specific co-inheritance relative to other traits. This in turn leads to their co-ordinated response to selection. Therefore, functional and developmental integration lead to genetic integration which, in turn leads to evolutionary integration. Three examples of how developmental integration structures pleiotropy and morphological variation in non-human primate crania, artificially-modified human crania, and for the effects ofindividual genes on murine mandibular morphology are presented.