This paper evaluates the performance of an automatic method for structural decomposition, noise removal and enhancement of bowel sounds (BS), based on the wavelet transform. The proposed method combines multiresolution analysis with hard thresholding to compose a wavelet transform-based stationary-nonstationary (WTST-NST) filter, for enhanced separation of bowel sounds (BS) from superimposed noise. Quantitative and qualitative analysis of the experimental results, when applying the WTST-NST filter to BS recorded from controls and patients with gastrointestinal dysfunction, prove that the ability of the WTST-NST filter to remove noise and reveal the authentic structure of BS is excellent. By eliminating the need to record a noise reference signal, this method reduces hardware overhead when analysis of BS is the primary aim. The method is independent of subjective human judgement for selection of noise reference templates, is robust to different levels of signal interference, and, due to its simplicity, can easily be used in clinical medicine.