The present invention is a method and apparatus for non-invasive, real-time monitoring of the autonomic nervous systems. The present invention allows for monitoring of the autonomic nervous system using spectral analysis of both heart rate and respiratory signals. A preferred embodiment uses short-time Fourier transform (STFT) with a novel modified Bartlett windowing scheme in real-time so that the dynamic interactions between the sympathetic and parasympathetic divisions of the autonomic nervous system can be independently monitored. In addition, a preferred embodiment of the present invention uses the same techniques to monitor other biological or physiological data, including continuous blood pressure.