Blood flow velocities were measured in both middle cerebral arteries (MCAs) of 36 healthy subjects using transcranial Doppler ultrasound. Measurements were first made using a hand-held probe. Velocities were then studied bilaterally with fixed probes under resting conditions and during simultaneous regional CBF (rCBF) measurements. A significant (p < 0.05) positive correlation was found between MCA flow velocities and rCBF in the estimated perfusion territory of this artery. The correlation coefficient was highest when the measurements were performed simultaneously (p < 0.001) or when velocities recorded with a hand-held probe were adjusted to take into account the significant velocity increase induced by the CBF study situation. The increased velocities during CBF measurements cannot be fully explained by the moderate but significant PCO2 increase. Other possible mechanisms are increased blood flow due to mental activation or MCA vasoconstriction secondary to stimulation of the sympathetic nervous system. The effect of mental activation and PCO2 differences should therefore be considered when comparing the results of repeated velocity and CBF measurements.