The aetiology of scaphocephaly is often described as premature fusion of the sagittal suture. This study observed wave-like deformations in abnormally long and narrow skulls typical of scaphocephaly, and these deformations were divided into two types: type I deformations (one wave) and type II deformations (two waves). However, the pathogeneses of these deformations are unknown. Computed tomographic data sets were retrospectively analyzed from 18 patients with scaphocephaly who were admitted to the hospital between 2000–2010. Using three-dimensional reconstructions of the computed tomographic images, the relationship was analysed between the wave deformation types and the state of the sutures and fontanelles. The results demonstrate that the type of wave deformation was dependent on the location of the sagittal suture closure. Specifically, the premature closure of the posterior half of the sagittal suture caused a type I deformation, while total closure resulted in a type II deformation (p < 0.001). It is hypothesized that restricted growth of the fused suture causes billowing, which results in a waving deformation. The deformities that are often observed in sagittal synostosis can be explained more accurately.