Introduction: Neonates requiring aortic arch repair are unable to maintain adequate oxygenation levels and require surgical intervention. A high percentage of survivors exhibit signs of neurological deficit possibly due to inadequate cerebral blood flow during surgery. Middle cerebral artery velocity (MCAv) using transcranial Doppler (TCD) provides information about perfusion. Our aim was to continuously monitor MCAv during aortic arch repair. Methods: MCAv was monitored in five neonates (age 19±6 days, body mass 3.6±0.6 kg) undergoing surgery on the aortic arch, alongside near infrared spectroscopy (NIRS), blood pH, pO2, pCO2, HCO3, lactate, Hb, Htc (%) and temperature (core and rectal). Using general linear models, MCAv was compared between initial sedation, cardiopulmonary bypass (CBP), cooling at 30, 25, 20, the lowest temperature, during selective cerebral perfusion, whole body perfusion, during rewarming at temperatures of 25, 30, 36, once off cardiopulmonary bypass and after surgery. MCAv was obtained for ‘healthy’ neonates (aged 2±1 days, body mass 3.5±0.6 kg) and used as a reference point. Results: During and following surgery MCAv was lower when compared to healthy neonates expect for during cooling. MCAv and NIRS changed during surgery (p=0.06). MCAv was 9.65, 14.9 and 13.1cm.s-1 higher during cooling when at 30, 25 and lowest temperature, respectively when compared to CBP (p=0.03). Once off CBP, MCAv returned to pre surgery values. Conclusion: Our data suggests that MCAv as a marker of cerebral perfusion is lower during cardiopulmonary bypass and higher during cooling. These changes could provide clinicians with information on how to optimise cerebrovascular health.