Computerized processes are supportive in the new age of medical treatment. Biomedical signals which are collected from the human body supply or important useful data that are related with the biological actions of human body organs. However, these signals may also contain some noise. Heart waves are commonly classified as biomedical signals and are non-stationary due to their statistical specifications. The probability distributions of the noise are very different, and for this reason there is no common method to remove the noise. In this study, adaptive filters are used for noise elimination and the transcranial Doppler signal is analyzed. The artificial bee colony algorithm was employed to design the adaptive IIR filters for noise elimination on the transcranial Doppler signal and the results were compared to those obtained by the methods based on popular and recently introduced evolutionary algorithms and conventional methods. (C) 2012 Elsevier Ltd. All rights reserved.