The authors report here a 3-year-old boy with localized absence of calvarial bones (partial acalvaria/hypocalvaria), associated with unique sagittal calcified bone and craniosynostosis. This major skull deformation led to a prominent protrusion of the cerebral hemisphere and other significant parenchymal changes that were well demonstrated by neuro-imaging. No digital abnormalities and only minor facial dysmorphism were observed; however, his development is grossly delayed. History and detailed investigations failed to explain the cause of his condition. Mutation testing of fibroblast growth factor receptor (FGFR) 1, 2 and 3 gave normal results. The combination of craniosynostosis and acalvaria in this surviving boy could be a rare presentation of a more lethal condition.