Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders and is that with the greatest socioeconomic impact worldwide. Diagnosis of IBS is based on clinical criteria that have been modified over time, the Rome II criteria being those that are currently followed. Some of the symptoms of IBS are similar to those in patients with inflammatory bowel disease (IBD), which can hamper or delay diagnosis. The use of inflammatory markers in stools (such as calprotectin) may help to distinguish between these two entities. A possible connection between IBS and IBD could be based on five points: (i) both disorders have similar symptoms; (ii) symptoms often overlap in the same patients; (iii) IBS and IBD have a common familial aggregation; (iv) some predisposing factors, such as a history of acute gastroenteritis, play a role in both disorders, and (v) importantly, signs of microinflammation are found in the bowels of patients with IBS. With regard to this latter point, an increase in inflammatory cells has been found in the intestinal mucosa of patients with IBS and, more specifically, mastocytes have been found to be increased in the jejunum and colon while CD3 and CD25 intraepithelial lymphocytes have be observed to be increased in the colon. Moreover, activated mastocytes are increased near to nerve endings in patients with IBS and this finding has been correlated with the intensity of both intestinal symptoms (abdominal pain) and psychological symptoms (depression and fatigue). A good model of microinflammation is post-infectious IBS, since the timing of the onset of the infectious process is known. In patients with post-infectious IBS, an increase in intraepithelial lymphocytes and enterochromaffin cells is initially found, which is reduced over time; consequently, although the symptoms of IBS persist, after 3 years no differences are detected in the number of inflammatory cells between IBS patients and controls. Among the various factors that can favor the development of IBS in these patients, two host-dependent mechanisms are most closely implicated in the physiopathology of IBS: polymorphism of the genes codifying pro- or anti-inflammatory cytokines and psychological factors such as anxiety, depression, somatization and neuroticism at the time of the acute infection. In view of all of the above, the similarities between IBS and IBD are probably more than mere coincidence and may reflect distinct manifestations of a broad spectrum of inflammation in the colon.