We present the MR imaging findings of a girl with horizontal gaze palsy and progressive scoliosis (HGPPS). HGPPS is a rare congenital disorder characterized by absence of conjugate horizontal eye movements and accompanied by progressive scoliosis developing in childhood and adolescence. MR imaging depicted brain-stem hypoplasia with absence of the facial colliculi, presence of a deep midline pontine cleft (split pons sign), and a butterfly configuration of the medulla. These MR imaging features suggest the diagnosis of HGPPS and correlate with the clinical findings. We hypothesize that maldevelopment of dorsomedial brain-stem structures plays a crucial role in the pathogenesis of HGPPS.