The analysis of heart rate variability, involving changes in the autonomic modulation conditions, demands specific capabilities not provided by either parametric or non-parametric spectral estimation methods. Moreover, these methods produce time-averaged power estimates over the entire length of the record. Recently, empirical mode decomposition and the associated Hilbert spectra have been proposed for non-linear and non-stationary time series. The application of these techniques to real and simulated short-term heart rate variability data under stationary and non-stationary conditions is presented. The results demonstrate the ability of empirical mode decomposition to isolate the two main components of one chirp series and three signals simulated by the integral pulse frequency modulation model, and consistently to isolate at least four main components localised in the autonomic bands of 14 real signals under controlled breathing manoeuvres. In addition, within the short time-frequency range that is recognised for heart rate variability phenomena, the Hilbert amplitude component ratio and the instantaneous frequency representation are assessed for their suitability and accuracy in time-tracking changes in amplitude and frequency in the presence of non-stationary and non-linear conditions. The frequency tracking error is found to be less than 0.22% for two simulated signals and one chirp series.