Hajdu-Cheney syndrome is a rare congenital disease with acro-osteolysis, osteoporotic changes of the spine and long bones of extremities and marked basilar invagination with an unusually deformed skull. Magnetic resonance imaging of a 32-year-old male revealed the deformed skull and almost horizontal basal angle and the elongated and upwardly shifted brain stem caused by the tip of the odontoid process of the second cervical vertebra invaginating the base of the skull. In addition there were atrophic pituitary gland, widely open sella turcica and symmetrical fluid collections along the optic nerve sheath.