Crouzon syndrome is characterised by premature fusion of cranial sutures and synchondroses leading to craniofacial growth disturbances. The gene causing the syndrome was discovered approximately a decade ago and recently the first mouse model of the syndrome was generated. In this study, a set of Micro CT scans of the heads of wild-type (normal) mice and Crouzon mice were investigated. Statistical deformation models were built to assess the anatomical differences between the groups, as well as the within-group anatomical variation. Following the approach by Rueckert et al. we built an atlas using B-spline-based nonrigid registration and subsequently, the atlas was nonrigidly registered to the cases being modelled. The parameters of these registrations were then used as input to a PCA. Using different sets of registration parameters, different models were constructed to describe (i) the difference between the two groups in anatomical variation and (ii) the within-group variation. These models confirmed many known traits in the wild-type and Crouzon mouse craniofacial anatomy. However, they also showed some new traits.