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 external EEnG 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 vs. 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.