This paper presents Multiresolution Adaptive Filter (MAF) for estimating brainstem auditory evoked potential (BAEP). Multiresolution Adaptive Filter is implemented simply by the orthonormal wavelet transforming(WT) the reference and primary signals, adaptive filtering of each independent, frequency channel separately, and then inverse wavelet transforming (IWT). Multiresolution adaptive processing can be employed as adaptive noise cancellation, adaptive line enhancer, and adaptive averaging. In this paper, we apply the MAF for BAEP estimation. The method is evaluated by using simulation and human data. A comparison of the proposed scheme with ensemble averaging and time-invariant adaptive filter (TIAF) is presented. It is observed that a significant improvement in waveform estimation, compared with the ensemble averaging and TIAF, can be achieved by multiresolution adaptive processing.