The deformities of craniofacial bones in brachycephaly (n = 2) and plagiocephaly (n = 2) were compared using three-dimensional skull replicas. In brachycephaly the bilateral deformities of the cranial base were similar to the unilateral deformities on the affected side in plagiocephaly. Shortening of the anterior-middle cranial fossas and expansion of the middle cranial fossas suggest downward and anterior displacement of both temporomandibular (TM) joints resulting in the underdevelopment of the middle-inferior facial bones, though this is less conspicuous in brachycephaly for three reasons. The most important one is that the patients have an imposing facial morphology characterised by high, protruding facial bones, as found on the affected side in plagiocephaly. Secondly, the frontal bones are flattened and positioned posteriorly in the anteroposterior direction, which also helps to mask the underdevelopment of the middle-inferior facial bones. Finally, as bony deformities are symmetrical in brachycephaly, they are not as obvious as they would be if they were unilateral.