Surface recording of electroenterogram (EEnG) is a non-invasive method for monitoring intestinal myoelectrical activity. However, surface EEnG is seriously affected by a variety of interferences: cardiac activity, respiration, very low frequency components and movement artefacts. The aim of this study is to eliminate respiratory interference and very low frequency components from external EEnG recording by means of empirical mode decomposition (EMD), so as to obtain more robust indicators of intestinal pacemaker activity from the external EEnG signal. For this purpose, 11 recording sessions were performed in an animal model under fasting conditions and in each individual session the myoelectrical signal was recorded simultaneously in the intestinal serosa and the external abdominal surface in physiological states. Various parameters have been proposed for evaluating the efficacy of the method in reducing interferences: the signal-to-interference ratio (S/I ratio), attenuation of the target and interference signals, the normal slow wave percentage and the stability of the dominant frequency (DF) of the signal. The results show that the S/I ratio of the processed signals is significantly greater than the original values (9.66 +/- 4.44 dB versus 1.23 +/- 5.13 dB), while the target signal was barely attenuated (-0.63 +/- 1.02 dB). The application of the EMD method also increased the percentage of the normal slow wave to 100% in each individual session and enabled the stability of the DF of the external signal to be increased considerably. Furthermore, the variation coefficient of the DF derived from the external processed signals is comparable to the coefficient obtained using internal recordings. Therefore, the EMD method could be a very useful tool to improve the quality of external EEnG recording in the low frequency range and therefore to obtain more robust indicators of the intestinal pacemaker activity from non-invasive EEnG recordings.