The geometric morphometrics method (GMM) is a technique to study scale and shape relationships of structures using Cartesian geometric coordinates rather than linear, areal (of area), or volumetric variables. GMM has been of great value in many biological studies, but does not appear to have been used to examine equine skulls.In this exploratory study, twenty-nine normal equine heads of three different age groups: <5 years old (N = 9), 6-15 years old (N = 10) and > 16 years old (N = 10) were examined.Computed tomography (CT) bone window DICOM images were reconstructed into isosurfaces (3-dimensional contoured surfaces), onto which landmarks were added using Stratovan Checkpoint® software. Data from 29 landmarks were analysed using MorphoJ analysis, which applies a Procrustes fit, prior to reducing data dimensionality through principal component (PC) analysis. PCs with and without allometry were considered. Allometric shape described by PC1 accounted for 27% of variance. Loading pertaining to: the pterygoid process, bilaterally; caudal aspect of hard palate; tip of nasal bone; ethmoid sinuses, bilaterally; caudal aspect of the ventral conchal bulla, bilaterally and caudal aspect of the vomer bone suggest that these anatomical structures are predictive of age group. When allometric effects (shape variation explained by size) were removed, PC1 was unable to distinguish horses by age group. Allometric shape differences could distinguish the youngest versus the two older age groups. The potential applications of GMM in equine diagnostic imaging are wide ranging and include the investigation of changes in the equine skull with respect to genetics and characterisation of conformation-related diseases affecting the teeth, jaws and sinonasal compartments.