In the analysis of epileptic electroencephalographic (EEG) and magnetoencephalography (MEG) data, spike separation is diagnostically important because localization of epileptic focus often depends on accurate extraction of spiky activity from the raw data. In this paper, we present a method to automatically extract spikes using the wavelet transform combined with morphological filtering based on a circular structuring element. Our experimental results have shown that this method is highly effective in spike separation. Comparisons with the wavelet, bandpass filter, empirical mode decomposition (EMD), and independent component analysis (ICA) methods show that the new method is more effective in estimating both spike amplitudes and locations.