Patients with irritable bowel syndrome have heightened perception of gut sensation. The mechanisms responsible for this remain unknown, due to current poor knowledge of the central processing of gut sensation. Cortical evoked potentials (CEPs) have been recorded following both electrical rectal stimulation (ERS) and mechanical rectal stimulation (MRS). Because of the lack of a direct comparison of these two methods, their robustness for future clinical use remains unknown. The aim of our study was to compare the characteristics of CEPs following ERS and MRS. CEPs were recorded from the vertex in 14 healthy volunteers following ERS with bipolar ring electrodes, and MRS by repeated rectal distension. CEPs were recorded in all subjects following electrical stimulation, but only in 11 subjects following mechanical stimulation. In comparison with electrical stimulation, mechanical stimulation produced CEPs with a smaller amplitude and longer latency. However, the morphology of CEPs following electrical and mechanical rectal stimulation was similar, with no difference in the interpeak latencies. In conclusion, we have demonstrated that electrical rectal stimulation is a more reliable stimulus for recording CEPs. The similarity of the morphology and interpeak latencies of the CEPs suggests that both stimuli are activating a similar network of cortical neurones.