The multiple possibilities for the application of Fast Fourier Transformation (FFT) in the cardiorespirography of neonates are shown as a summary of our own results. The basis is the power spectral analysis of instantaneous heart rate and respiratory movements, which can be complemented by a coherence analysis of both parameters. A model-aided method for quantification of respiratory sinus arrhythmia (RSA) as an additional application for power spectral and coherence analysis is discussed. The realization of Hilbert transformation by FFT makes possible the interval-related calculation of respiration rate. The necessity of this supplementation, as well as the resulting strategies of additional processing steps are emphasized. The results is a concept of signal processing which increases the efficiency of previously employed methods in computer-aided cardiorespirography.