The aim of this study was to assess the reliability of cortical evoked potentials after electrical stimulation of the anal canal. Cortical evoked potentials were recorded on 243 patients presenting with perineal pain (28 patients), impotence (55 patients), anal incontinence (52 patients), urinary continence (30 patients), constipation (49 patients), and on 29 neurological patients, by stimulating the external anal sphincter and penis (or clitoris). The inter- and intra-observer reproducibility was studied by coding recordings interpreted by three different observers on two separate occasions. The influence of recording characteristics and clinical data were assessed. To study operator dependence, five operators investigated the patients. Only one of them was well trained in this technique. The interpretation of the coded curves by the observers was poorly reproducible in about 15% of cases, depending on time between the two readings and the quality of recordings. The interpretation of cerebral responses after anal stimulation were observer-dependent and influenced by the knowledge of clinical data. This was also observed with cortical evoked potentials after electrical stimulation of the penis or clitoris, but to a lesser extent. The cerebral evoked potentials method was also operator-dependent, mainly after anal stimulation. When a study of cortical evoked potentials by perineal stimulation is needed in clinical practice, it seems logical to prefer cortical evoked potentials by penile or clitoral stimulation as they seem easier to obtain than those evoked by anal stimulation if the investigators are not well trained for the performance of electrophysiological studies as the former are much less operator- and observer-dependent.