The dynamic response of cerebral autoregulation to spontaneous changes in arterial blood pressure (ABP) is described by the relationship between cerebral blood flow velocity (CBFV) and resistance-area product (RAP). CBFV was measured with Doppler ultrasound in the middle cerebral artery and ABP with an intra-arterial catheter in 66 neonates. Spontaneous changes in mean ABP were automatically detected and the maximum derivative was used to synchronize the coherent averaging of corresponding CBFV and RAP transients. These were classified into two groups corresponding to intact (group A) or impaired (group B) autoregulation. The cross correlation between RAP and CBFV indicates a significant relationship with a time delay of 5 s for group A. The frequency response of RAP was estimated by the cross spectra with CBFV. Groups A and B present a similar amplitude spectra but the phase spectra of group A lags that of group B. The impulse responses of the two groups are also markedly different and were used to simulate the velocity response to a 5% step change in ABP. Impulse responses were also obtained for four different levels of pCO2 showing that hypercapnia leads to an impulse response similar to that of group B (impaired autoregulation). This method can be used to extend the usual dichotomic classification adopted in clinical studies of autoregulation.