Hypophosphatemic rickets (HR) are diseases characterized by deficient mineralization of bone due to abnormal renal wasting of phosphate. Deformation of bony structures of cartilaginous origin has been described as a major characteristic in patients with HR, but little is known about the impact on bony structures of intramembranous origin. The aim of the present study was to describe the osseous morphology of the craniofacial structures in patients with HR compared to healthy controls, and to investigate the impact of different bone origin on the osseous morphology. Fifty-three patients with HR (17 males, 36 females), aged 3-74 yrs, were included. Fifty HR patients had dominant X-linked disease, and in three patients no mutations were identified. A total of 79 healthy individuals (37 males, 42 females), aged 6-79 yrs, with normal occlusion served as controls. Significant cephalometric differences were found between HR patients and controls. In HR patients, the cranial base was flattened and the depth of the posterior cranial fossa was decreased. The anterior height of the cranium, the angle nasion-sella-frontale, and the thickness of theca were increased. The length of the nasal bone and the height of the maxilla were reduced. In contrast, the vertical as well as the sagittal relation between the jaws were unaffected in HR patients compared to controls. In conclusion, we found that the cranial structures of cartilaginous origin as well as the structures of intramembraneous origin were affected in patients with HR.