The work contains a review of modern methods and tools used to study the regulation of human cerebral circulation. The first part discusses the basic concepts of the mathematical description of regulatory processes based on the biomedical signals analysis. The Fourier transform and transfer function, signal coherence, convolution of functions, correlation analysis, fractal analysis, wavelet transform, artificial neural networks, Hilbert – Huang transform are presented. The second part is devoted to the papers where these methods were used for medical examinations. Their analysis showed that there was a discussion of specialists regarding the choice between linear and nonlinear models of functioning the cerebral blood flow autoregulation system. It was concluded that there was currently no single approach to solving the problem, and there remains a need to continue the development of new methods and models and their implementation in medical practice.