We introduce the Ontology of Craniofacial Development and Malformation (OCDM), a project of the NIH-funded FaceBase consortium, whose goal is to gather data from multiple species, at levels ranging from genes to gross anatomy, in order to understand the causes of craniofacial abnormalities. The OCDM is being developed in order to facilitate integration of these diverse forms of data in a central Hub. It currently consists of several components, including human adult and developmental anatomy, corresponding mouse structures, and malformations. Example queries show the potential of the OCDM for intelligent data annotation and querying.