The purpose of this study was to examine cerebral autoregulation (CA) in young athletes experiencing concussion. The subjects were monitored and repeatedly tested 72 hours, 2 weeks and 1 month post-injury. Mean arterial blood pressure (MABP), end-tidal partial pressure of carbon dioxide (PETCO2) and cerebral blood flow velocity (CBFV) in the middle and posterior cerebral arteries were monitored during mental activation paradigms. In order to characterize CA we employed autoregressive models with exogenous inputs (ARX) and impulse response models based on the Laguerre expansion technique (LET). By extracting gain and phase estimates from the obtained models we were able to detect disruptions in CA 72 hours following concussion and a slow recovery within a time period of one month.