We examined the use and potential of quantifying instantaneous heart rate variability (HRV) using a joint time-frequency and time-domain methods. These new techniques are promising, because they provide tools to quantify nonstationary, beat-by-beat changes in HRV components, and are therefore flexible with respect to the design of experimental protocols. A smoothed pseudo-Wigner–Ville distribution (SPWVD) and a time-domain index using polynomial filtering produced fairly coherent estimates of band-specific HRV amplitudes, whereas SPWVD yielded additional information on the frequency characteristics of HRV. Instantaneous HRV appeared to have a complex and a frequency-specific relationship to cardiac activity and electrodermal activity. It is concluded that the time-frequency analysis of HRV is a very promising method for mapping transient changes in the frequency and amplitude characteristics of cardiac dynamics.