The myenteric plexus undergoes adaptive changes under several conditions. Mucosal and muscular alterations of the colon have been described after fecal stream diversion but studies concerning the myenteric plexus after this procedure are scarce. Therefore, 28 Wistar rats were submitted to fecal diversion and followed for different periods (30, 60, 120 and 180 days), in order to study the myenteric plexus of the excluded segments. Seven non-operated rats were employed as control. The myenteric plexus was subsequently evaluated with the NADH and NADPH histochemical techniques. The colonic area of excluded segments is significantly decreased. The density of NADH-stained neurons continuously increases during the entire postoperative period but does not match the extent of surface reduction. Neuronal area measurements suggest hypertrophy of the remaining neurons in the late postoperative period. Morphological alterations of myenteric ganglia and neurons were also evident. An important surface area reduction combined with slight density increase points toward significant neuronal loss after fecal diversion. While studies correlating neuronal loss and functional changes are still lacking, surgeons should bear in mind the modifications of the myenteric plexus when performing fecal stream diversion surgeries.