Objectives This study aimed to investigate differences and demonstrate a normal range of morphological variation of the caudal fossa of the cranium of domestic cats. Methods CT scans of 32 domestic cat heads of 11 breeds were included. Isosurfaces from skulls were characterised through three-dimensional geometric morphometrics using geographical landmarks placed on the internal surface of the caudal fossa and foramen magnum. Raw data was transformed with a Procrustes fit and coordinate covariance was analysed by principal components to establish breed- and sex-level differences. Skulls were also classified according to the number of concavities along the mid-sagittal vermiform impression. Differences were investigated between breed groups and sex, and correlation was sought with age. Results Analyses revealed size-independent differences in occipital bone morphology across breeds and sex; however, no clustering was evident. Most variability was observed at the exoccipital bones, ventral portion of the supraoccipital bone, dorsum sellae of the basisphenoid and the osseous tentorium cerebelli. No statistically significant differences were identified via two-sample t-tests between breed groups or sexes. No statistically significant correlation using Spearman rho correlation coefficient was identified with age. Conclusions and relevance The feline caudal fossa displays a wide range of intra- and inter-breed variation, not linked to age or sex. Concavities along the vermiform impression have not previously been described. As advanced imaging modalities are becoming more frequently used for domestic felids, an established range of normality is important for discriminating pathological changes from anatomical variances.