We examined changes in the blood flow velocity of brain stem artery (BSA) and middle cerebral artery (MCA) in response to hypercapnic, normocapnic and hypocapnic hyperventilation in seven awake subjects with a transcranial Doppler to determine if there are differences in blood flow control in regional brain perfused by these respective arteries, and to separate the effects of CO2 and ventilation itself on blood flow velocity during CO2 loading. During hypercapnic hyperventilation, BSA flow velocity increased linearly with an increase in end-tidal partial pressure of CO2 (PETCO2). During hypocapnic hyperventilation, BSA flow velocity decreased linearly with decrease in PETCO2, but did not change during normocapnic hyperventilation. The mean CO2 reactivity of BSA was 2.8%/mmHg. The responses of MCA to these hyperventilations and CO2 reactivity were similar to those of BSA. These findings suggest that CO2 rather than ventilation per se is the important stimulus to changes in brain blood flow velocity and that the CO2 responses of brain arteries are not affected by differences in vascular beds.