Most signal averaging processes used for cardiac signals align successive waveforms using a template matching process. In addition to achieving accurate temporal alignment of the signals, this operation must also ensure that the signal average comprises signals of the same morphology. For P wave signal averaging, systems designed for QRS complex averaging are often used, with the template acquisition window shifted to include the P wave. Theoretically, with this technique, variations in P wave morphology could reduce the high frequency content of the signal. We tested this hypothesis by comparing the performance of a selective P wave averaging system with a conventional system, based on template matching by cross-correlation over a fixed acquisition window, on identical P wave recordings from 15 subjects. The selective system identifies variations in P wave morphology and generates up to five candidate templates for averaging. Subsequently, the most frequently matched template over a 100-beat sample is used for averaging. Only P waves with the same morphology as this template are averaged. Selective averaging mainly increased the measured high frequency P wave energy, without affecting P wave duration after high pass filtering at 40 Hz, (Duration: 157(4)ms selective vs 155(4) nonselective. Energy 80-150 Hz: 1.77(0.28), microV2.s selective vs 1.61(0.3) microV2.s non selective, P < 0.01). These observations confirm that nonselective P wave averaging can reduce apparent P wave energy, especially at high frequency. Before meaningful studies of the value of frequency domain analysis of the P wave can be performed, it is important that signal averaging systems of sufficient fidelity are utilized.