A method called modified time-sequenced adaptive filtering (MTSAF) is applied to estimate evoked potential (EP) signals and track the temporal variations of EPs. The MTSAF consists of a set of adaptive filters (AFs), with each processing a time segment of EP data. After convergence, each AF reaches the best estimation of EP signals over its own time segment in terms of minimum mean squared error (MMSE). Numerical results of simulated and human EP data show that the MTSAF reaches better estimation of EPs than a conventional adaptive signal enhancer (ASE). With the MTSAF, the temporal variations of EPS across trials can be estimated to reveal more subtle variations of EPs, which may be of clinical value.