In this paper, we use a new approach based on Simulated Annealing for estimating the BAEPs (brainstem auditory evoked potentials). Each BAEP is obtained through a hundred of responses to stimulations. In case of endocochlear pathologies, it has been assumed that these signals could be randomly delayed from a response to another one. In such cases, the application of the averaging method systematically leads to "smoothed" BAEPs, thus complicating both identification and interpretation operations. The method presented in this paper consists in minimizing a non linear criterion in order to obtain an alignment of the various responses, before averaging them. Simulated and experimental results are presented, and compared to those produced by the classical method.