Quantification of nonlinear interactions between two nonstationary signals presents a computational challenge in different research fields, especially for assessments of physiological systems. Traditional approaches that are based on theories of stationary signals cannot resolve nonstationarity-related issues and, thus, cannot reliably assess nonlinear interactions in physiological systems. In this review we discuss a new technique "Multi-Modal Pressure Flow method (MMPF)" that utilizes Hilbert-Huang transformation to quantify dynamic cerebral autoregulation (CA) by studying interaction between nonstationary cerebral blood flow velocity (BFV) and blood pressure (BP). CA is an important mechanism responsible for controlling cerebral blood flow in responses to fluctuations in systemic BP within a few heart-beats. The influence of CA is traditionally assessed from the relationship between the well-pronounced systemic BP and BFV oscillations induced by clinical tests. Reliable noninvasive assessment of dynamic CA, however, remains a challenge in clinical and diagnostic medicine.In this brief review we: 1) present an overview of transfer function analysis (TFA) that is traditionally used to quantify CA; 2) describe the a MMPF method and its modifications; 3) introduce a newly developed automatic algorithm and engineering aspects of the improved MMPF method; and 4) review clinical applications of MMPF and its sensitivity for detection of CA abnormalities in clinical studies. The MMPF analysis decomposes complex nonstationary BP and BFV signals into multiple empirical modes adaptively so that the fluctuations caused by a specific physiologic process can be represented in a corresponding empirical mode. Using this technique, we recently showed that dynamic CA can be characterized by specific phase delays between the decomposed BP and BFV oscillations, and that the phase shifts are significantly reduced in hypertensive, diabetics and stroke subjects with impaired CA. In addition, the new technique enables reliable assessment of CA using both data collected during clinical test and spontaneous BP/BFV fluctuations during baseline resting conditions.