Support Vector Machines (SVM) have been applied extensively to classification and regression problems, but there are few solutions proposed for problems involving time-series. To evaluate their potential, a problem of difficult solution in the field of biological signal modeling has been chosen, namely the characterization of the cerebral blood flow autoregulation system, by means of dynamic models of the pressure-flow relationship. The results show a superiority of the SVMs, with 5% better correlation than the neural network models and 18% better than linear systems. In addition, SVMs produce an index for measuring the quality of the autoregulation system which is more stable than indices obtained with other methods. This has a clear clinical advantage. © Springer-Verlag Berlin Heidelberg 2006.