The aim of this study was to assess the error made by violating the assumption of stationarity when using Fourier analysis for spectral decomposition of heart period power. A comparison was made between using Fourier and Wavelet analysis (the latter being a relatively new method without the assumption of stationarity). Both methods were compared separately for stationary and nonstationary segments. An ambulatory device was used to measure the heart period data of 40 young and healthy participants during a psychological stress task and during periods of rest. Surprisingly small differences (<1%) were found between the results of both methods, with differences being slightly larger for the nonstationary segments. It is concluded that both methods perform almost identically for computation of heart period power values. Thus, the Wavelet method is only superior for analyzing heart period data when additional analyses in the time-frequency domain are required.