We report on a patient with brainstem disconnection associated with periventricular nodular heterotopia and bilateral proatlantal intersegmental arteries. The patient was a girl born after 37 weeks of gestation with birth weight of 1,938 g. Polyhydroamnios and lack of swallowing movement were noted on fetal ultrasonography. No spontaneous body movement or respiration was observed after birth, whereas facial movement was preserved. She had marked generalized weakness and absent deep tendon reflexes. She remains alive and hospitalized at 4 years of age but requires mechanical ventilation and feeding through a gastrostomy tube. MRI showed absence of the lower pons and the medulla oblongata associated with hypoplasia of the cerebellar vermis and hemispheres. In addition, ventriculomegaly and periventricular nodular heterotopia were observed in the cerebrum. MR angiography demonstrated the absence of vertebral arteries and presence of bilateral proatlantal intersegmental arteries arising from the external carotid arteries. Array-comparative genomic hybridization analysis did not show any genomic copy number aberrations. No mutation was found in the FLNA gene or the EN2 gene. The constellation of the malformations of our patient suggested that genes related to the development of the central nervous and vascular system may be involved in the pathogenesis of brainstem disconnection. © 2009 Wiley-Liss, Inc.