Congenital central hypoventilation syndrome (CCHS) patients show hypoventilation during sleep and severe autonomic impairments, including aberrant cardiovascular regulation. Abnormal sympathetic patterns, together with increased and variable CO(2) levels, lead to the potential for sustained cerebral vasculature changes. We performed high-resolution T1-weighted imaging in 13 CCHS and 31 control subjects using a 3.0-T magnetic resonance imaging scanner, and evaluated resting basilar and bilateral middle cerebral artery cross-sections. Two T1-weighted image series were acquired; images were averaged and reoriented to common space, and regions containing basilar and both middle cerebral arteries were oversampled. Cross-sections of the basilar and middle cerebral arteries were manually outlined to calculate cross-sectional areas, and differences between and within groups were evaluated. Basilar arteries in CCHS were significantly dilated over control subjects, but both middle cerebral artery cross-sections were similar between groups. No significant differences appeared between left and right middle cerebral arteries within either group. Basilar artery dilation may result from differential sensitivity to high CO(2) over other vascular beds, damage to serotonergic or other chemosensitive cells accompanying the artery, or enhanced microvascular resistance, and that dilation may impair tissue perfusion, leading to further neural injury in CCHS.