The aim of the chapter is to review aspects of the analysis of cardio-respiratory interaction using spectral estimation methods. The first section of the paper provides background on nonlinear physiological oscillation, entrainment phenomena and computer modelling. Entrainment phenomena are described in some detail including: frequency pulling and nonlinear modulation. These phenomena are illustrated using the examples of respiratory sinus arrhythmia and the baro-receptor reflex. ARMA and AR techniques are reviewed and compared to the FFT. Experimental results on the interaction of heart rate, blood pressure and respiration are presented; it was shown that ARMA techniques provided evidence of short term independent physiological mechanisms whereby respiration affects heart rate and blood pressure. In the second section of the chapter time-frequency representations are introduced and the Short-Term Fourier Transform (STET), Wigner–Ville Distribution (WVD) and wavelet transforms are compared on a theoretical basis and applied to heart rate and respiration data, as well as test data, to highlight their differences. The first section of this part of the chapter points out a number of apparently complex phenomena in blood pressure, respiration and heart rate waveforms. These phenomena were shown to be more clearly understood by the application of nonlinear dynamic theory, coupled to computer modelling. In the second section the main advantages of the time-frequency methods were highlighted. These are their robustness and the fact that these methods do not require the data being analyzed to be stationary and as such represent an important development in the beat-to-beat study of cardio-respiratory control.