Craniosynostosis, a disorder in which one or more fibrous joints of the skull fuse prematurely, causes skull malformation and may be associated with increased intracranial pressure and developmental delays. In order to perform medical research studies that relate phenotypic abnormalities to outcomes such as cognitive ability or results of surgery, biomedical researchers need an automated methodology for quantifying the degree of abnormality of the disorder. This paper addresses that need by proposing a set of features derived from CT scans of the skull that can be used for this purpose. A thorough set of experiments is used to evaluate the features as compared to two human craniofacial experts in a ranking evaluation.