The effects of hypercapnia on the intensity and phase of near infrared light back-scattered by the head were studied on eight healthy humans and two patients affected by monohemispheric lesions in the Middle Cerebral Artery (MCA) territory. A decrease in the light intensity and a variation of the phase were detected in all healthy subjects during apnea and hypercapnia. Only negligible changes were observed in the affected hemisphere of the patients. A concomitant study by Transcranial Doppler Sonography (TCD) showed an increase of the blood flow during hypercapnia both in normal hemispheres and, to a less extent, in the affected hemisphere of patients. This suggests that NIRS (Near Infrared Spectroscopy) is more sensitive to alterations of more cortical brain vascular system than TCD which is mainly testing MCA in the depth.