Two methods for single-trial analysis were compared, an established parametric template approach and a recently proposed non-parametric method based on complex bandpass filtering. The comparison was carried out by means of pseudo-real simulations based on magnetoencephalography measurements of cortical responses to auditory signals. The comparison focused on amplitude and latency estimation of the M100 response. The results show that both methods are well suited for single-trial analysis of the auditory evoked M100. While both methods performed similarly with respect to latency estimation, the non-parametric approach was observed to be more robust for amplitude estimation. The non-parametric approach can thus be recommended as an additional valuable tool for single-trial analysis.