Background: Carotid endarterectomy (CEA) is the first-line treatment in severe carotid stenosis to prevent stroke. Because of methodological limitations, the acute impact of CEA on baroreflex function and cerebral autoregulation is not well defined and was therefore investigated by applying a novel algorithm. Methods and Results: Systemic arterial blood pressure, ECG and respiration during metronomic breathing and Valsalva maneuver were continuously recorded in 18 patients with carotid stenosis before and after CEA, and in 10 healthy controls. Baroreflex sensitivity, frequency spectra of RR intervals and indices for cerebral autoregulation were evaluated by trigonometric regressive spectral analysis. Compared with the controls, patients had impaired baroreflex sensitivity. Baroreflex sensitivity and frequency spectra were not changed by CEA. Cerebral autoregulation of patients with carotid stenosis as calculated by phase shift was reduced compared with controls but it improved significantly after CEA. Improvement of cerebral autoregulation was independent of changes in cerebral blood flow velocity. Conclusions: Baroreflex sensitivity and cerebral autoregulation are impaired in patients with carotid stenosis, conferring a high stroke risk. CEA improves cerebral autoregulation, but does not affect baroreflex sensitivity. For further risk reduction, interventional approaches targeting baroreflex function need to be considered.