Rectal prolapse is associated with diminished anal sensitivity and rectal motor activity. Both sensory and motor functions are controlled by the extrinsic and intrinsic (enteric nervous system) innervation of the gastrointestinal tract. Studies of changes in intestinal innervation in humans and in animal models with rectal prolapse are extremely scarce. The Winnie mouse model of spontaneous chronic colitis closely represents human inflammatory bowel disease and is prone to develop rectal prolapse. We have investigated changes in the myenteric and inhibitory motor neurons and evaluated changes in the density of sensory afferent, sympathetic, and parasympathetic fibers in the rectal colon of Winnie mice with and without rectal prolapse. Our results demonstrate that rectal prolapse in Winnie mice with chronic colitis is correlated with enhanced levels of inflammation, gross morphological damage, and muscular hypertrophy of the rectum. Animals with prolapse have more severe damage to the rectal innervation compared with Winnie mice without prolapse. This includes more severe neuronal loss in the myenteric plexus, involving a decrease in nNOS-immunoreactive neurons (not observed in Winnie mice without prolapse) and a more pronounced loss of VAChT-immunoreactive fibers. Both Winnie mice with and without prolapse have comparable levels of noradrenergic and sensory fiber loss in the rectum. This is the first study providing evidence that the damage and death of enteric neurons, including nitrergic neurons in myenteric ganglia and the loss of cholinergic nerve fibers, are important factors in structural changes in the rectum of mice with rectal prolapse.