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The time-domain signals representing the heart rate variability (HRV) in the presence of an ectopic beat exhibit a sharp transient at the position of the ectopic beat, which corrupts the signal, particularly the power spectral density (PSD) of the HRV. Consequently, there is a need for correction of this type of beat prior to any HRV analysis. This paper deals with the PSD estimation of the HRV by means of the heart timing (HT) signal when ectopic beats are present. These beat occurrence times are modeled from a generalized, continuous time integral pulse frequency modulation model and, from this point of view, a specific method for minimizing the effect of the presence of ectopic beats is presented to work together with the HT signal. By using both, a white noise driven autoregressive model of the HRV signal with artificially introduced ectopic beats and actual heart rate series including ectopic beats, the more usual methods of HRV spectral estimation are compared. Results of the PSD estimation error function of the number of ectopic beats are presented. These results demonstrate that the proposed method has one order of magnitude lower error than usual ectopic beats removal strategies in preserving PSD, thus, this strategy better recovers the original clinical indexes of interest.