Migraine with aura (MA) is associated with changes in cerebral blood flow (CBF), whereas the role of cerebral autoregulation is uncertain. This study aimed to evaluate basal CBF, cerebral blood volume (CBV) and vasomotor reactivity (VMR) in MA patients. Twenty-one controls and 16 MA patients (eight with side predominance) underwent simultaneous examination of flow velocity in the middle cerebral arteries by transcranial Doppler (TCD) and of near-infrared spectroscopy (NIRS) parameters [oxygen haemoglobin saturation: oxygen%, and total haemoglobin content (THC)] at rest and after hypercapnia. Cerebral VMR, THC and oxygen% increases were significantly greater on the predominant compared with the non-predominant migraine side, with both sides of patients without side predominance and with controls. These findings suggest altered autoregulation in MA patients, possibly secondary to impaired cerebrovascular autonomic control. Simultaneous TCD and NIRS investigation could represent a non-invasive approach to evaluate cerebral haemodynamics at the cortical and subcortical level.