A 6-month-old boy with persistent primitive trigeminal artery (PPTA) presented with stridor, dysphagia, delayed motor development and postural neck and shoulder dystonia. Magnetic resonance imaging/angiography and ultrasonography revealed PPTA, with flow from the dilated basilar artery to the right internal carotid artery, lower brainstem compression by the dilated basilar artery, and cerebellar vermis hypoplasia. Evoked potentials showed lower pons and medulla oblongata functional disruption. These lesions may be related to vascular etiology in the lower brainstem or to congenital malformation syndrome involving infratentorial structures. The relationship of this condition to Möbius syndrome is discussed.