Accurate signal estimation by means of coherent averaging techniques needs temporal alignment methods. A known low-pass filtering effect is yielded when alignment errors are present. This is very critical in the estimation of low-level high-frequency potentials in high-resolution ECG analysis. A comparative study of the performance of three alignment methods (the double-level method, a new time-delay estimation method based on normalized integrals, and matched filtering) is presented in this paper. A real signal and additive random noise for several signal-to-noise ratios (SNR's) are selected to make an ensemble of computer-simulated beats. The relation between the standard deviation of temporal misalignment versus SNR is discussed. A second study with real ECG signals is also presented. Several morphologies of QRS and P waves are tested. The results are in agreement with the computer simulation study. Nevertheless, the power spectrum of the noise process can affect the results. Matched filter estimation has been tested in the presence of power line interference (50 Hz), with poor results. An application of the three alignment methods as a function of the SNR is proposed. The new time-delay estimation method has been observed to be robust, even in the presence of nonwhite noise.