Irritable bowel syndrome is a common disorder defined by a symptom complex including abdominal pain and altered bowel habit. The etiopathogenesis appears to be multifactorial and to involve altered gastrointestinal motor function, enhanced perception of visceral stimuli and psychosocial factors. More recently a role for mucosal immune activation has been suggested. Routine histologic examination reveals no mucosal abnormality in the majority of cases but quantitative histological, immunohistochemical and ultrastructural analyses reveal subtle morphologic changes involving lymphocytes, mast cells, enterochromaffin cells and enteric nerves. The recent appreciation of these changes has led to new hypotheses linking central and enteric nervous systems to immune processes. This review highlights the spectrum of morphologic changes that occur in irritable bowel syndrome, examines their relationship to the pathophysiology of irritable bowel syndrome and considers their relevance to daily pathology practice.