Cerebral haemodynamics and the level of serum 5-hydroxytriptamine (5-HT) were analysed in 21 migraine patients (8 with and 13 without aura) during the headache-free period as well as the attack. Cerebral vasoreactivity was evaluated by acetazolamide test and Transcranial Doppler ultrasonography (TCD). TCD findings were within normal ranges in the majority of migraine patients. Patients with migraine without aura had higher blood flow velocities (BFV) than patients with aura. Comparison of BVF and pulsatility index (PI) data patterns in migraine with and in migraine without aura during the attack revealed differences indicating cerebral hypoperfusion. It was noticed that systolic BFV decreased in migraine with aura on the headache side while PI increased. In migraine without aura, both systolic BFV and PI increased. 5-HT findings were heterogeneous. Reduction of cerebral vasoreactivity was observed especially in migraine with aura. Our results suggest different pathogenic mechanisms between migraine with and without aura, supporting the neurogenic inflammation theory.