The functional gastrointestinal disorders and the irritable bowel syndrome, in particular, represent one of the commonest causes of medical consultation and the most frequent diagnosis raised by the gastroenterologists. Despite their high prevalence, the aetiology and pathophysiology of these functional digestive disorders remains unclear and specific diagnostic markers and clearly effective therapeutic options are lacking as well. These factors generate an important impairment in the quality of life in these patients and a growing sanitary burden. Recent studies showing the presence of low grade intestinal mucosal inflammation along with mast cell hyperplasia may contribute to the development and perpetuation of visceral hypersensitivity and dismotility patterns and epithelial barrier abnormalities, characteristic of the irritable bowel syndrome. In this article we will review the role of the stress-mast cell axis in the modulation of the gut mucosal inflammation and in the pathophysiology of the irritable bowel syndrome.