Abstract: The evoked potential processing system includes, in one embodiment, a spectral averaging method. Time based, digital pre-stimulus and post-stimulus electroencephalographic (EEG) signal streams are obtained and are converted into frequency spectrum signals. A differential spectrum is obtained. The differential spectrums from a plurality of sweeps are summed. The summed differential spectrum is then converted into a time based signal stream which contains the evoked potential (EP) signal therein. The EP signal can also be obtained utilizing a two-dimensional filter. Pre- and post-stimulus EEG signal streams for a sub-group of stimuli, wherein each stimulus in a group has the same intensity or frequency, are filtered by conventional averaging or spectral differential averaging. The time based, filtered, post-stimulus EEG signal streams are placed in an array and the array is then filtered by a two-dimensional Fast Fourier Transform (FFT) filter.