The function of the Cerebral Blood Flow Autoregulation (CBFA) system is to maintain a relatively constant flow of blood to the brain, in spite of changes in arterial blood pressure. A model that characterizes this system is of great use in understanding cerebral hemodynamics and would provide a pattern for evaluating different cerebrovascular diseases and complications. This work posits a non-linear model of the CBFA system through the evaluation of various types of neural networks that have been used in the field of systems identification. Four different architectures, combined with four learning methods were evaluated. The results were compared with the linear model that has often been used as a standard reference. The results show that the best results are obtained with the FeedForward Time Delay neural network, using the Levenberg-Marquardt learning algorithm, with an improvement of 24% over the linear model (p<0.05). © Springer-Verlag Berlin Heidelberg 2005.