Computer-assisted medical imaging technologies provide new tools for the study of congenital craniofacial deformities. Three-dimensional surface reconstructions have been developed to simplify the interpretation and improve the utility of CT scans of the head. While 3-D reconstructions initially were applied to assist clinical management of craniofacial deformities, these images now are finding utility in the study of unique anomalies, the definition of group characteristics for dysmorphic heads, the differentiation of similar phenotypes, and the documentation of the effects of cranial surgery on craniofacial growth. These findings should assist the formulation and evaluation of hypotheses regarding mechanisms of congenital malformation and deformation.