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Background The analysis of abdominal sounds can help to diagnose gastro-intestinal diseases. Sounds originating from the stomach and the intestine, the so-called bowel sounds, occur in various forms. They are described as loose successions or clusters of rather sudden bursts. Realistic recordings of abdominal sounds are contaminated with noise and artifacts from which the bowel sounds must be differentiated. Methods The proposed intrinsic mode function-fractal dimension (IMF-FD) filtering utilizes the property of the multivariate empirical mode decomposition (MEMD) to behave as a series of band pass filters. The MEMD decomposes the abdominal signal into its different frequency components. The resulting intrinsic mode functions (IMFs) are modulated in amplitude and frequency where transient sonic events occur. Based on the complexity of the IMFs, measured by their fractal dimension (FD) in sliding windows, the information-carrying IMFs are selected. The filtered signal is formed as the superposition of all selected IMFs. The IMF-FD filter not only enhances the non-linear components of the original signal but also segments them from the rest. Another important aspect of this work is that typical artifacts that occur in the same frequency range as bowel sounds can be subsequently eliminated by heuristic rules. Conclusions The method is tested on a realistic, contaminated data set with promising performance: close to 100% of the manually labeled bowel sounds are identified. © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)