Moebius syndrome (MS) is described in an infant with central hypoventilation and brainstem calcification. The patient had limb defects and bilateral paralysis of the 6th, 7th, 9th, 10th, and 12th cranial nerves. Mechanical ventilation was continued from birth because of shallow spontaneous respiration. Computed tomography revealed brainstem atrophy and four small calcifications restricted to the dorsal portion of the pons and medulla. Prenatal brainstem injury such as ischaemia may have caused MS and central hypoventilation.