Visceral hypersensitivity is highly prevalent in most functional bowel disorders, such as irritable bowel syndrome (IBS), and activation of intestinal mast cells (MC) may play a role because they have been found in close proximity to gastrointestinal mucosal sensory nerve terminals containing neuropeptides and a bi-directional pathway connecting the central nervous system, gut, and MC has been demonstrated. The current study appraised the status of rectal visceral perception, as well as the changes in the MC and substance P (SP) in the intestinal mucosa of patients with IBS. The study group comprised 42 patients with IBS and 19 healthy subjects who underwent anorectal manometry and rectal perception thresholds to balloon distension. The MC and the SP-ergic terminals in the mucosa were stained for respective histochemical and immunohistochemical investigations. The results were presented both qualitatively and quantitatively by color image analyzer, based on analysis of the intensity and area of stained fibrils. The structural relationship between the MC and nerve terminals was studied by electron microscopy, using an in situ embedding technique. The anorectal resting pressure, squeezing pressure and relaxation pressure were normal in both groups. The sensation threshold, defecation threshold and pain threshold in diarrhea-predominant IBS and the pain thresholds in constipation-predominant IBS were much lower than in the controls. Rectal compliance decreased in IBS. The number of MC in the terminal ileum, the ileocecal junction and the ascending colon was significantly elevated in IBS (P < 0.01), and the MC showed great variation. A significantly increased concentration of SP was found in the colon of the IBS patients compared with the controls. There was a positive correlation between the profiles of mucosal MC and the SP-ergic terminals, and MC were closely adjacent to SP-ergic terminals in the lamina propria. As altered rectal perception is present in almost all patients with IBS, it might be a reliable biological characteristic of the disease. Alterations in the MC and SP of the intestinal mucosa may be important factors in visceral hypersensitivity.