Background Irritable bowel syndrome (IBS) is characterized by chronic gastrointestinal dysfunction in the absence of detectable organic disease. The recently developed technique, video capsule endoscopy (CE), has been shown to be much more sensitive than traditional enterography in detecting mucosal changes in the small intestine. This study was performed to see if any earlier, not detectable by other standard methods, mucosal changes could be found in the small intestine in patients diagnosed as having IBS. Methods All consecutive women who, over the past five years, had received a well-founded diagnosis of IBS at the Department of Medicine were identified. Twenty-eight women, mean age 36 ± 12 years were willing to participate in the study. They underwent a CE after a pre-test with a dummy capsule. The actual IBS activity was estimated by the validated Gastrointestinal Symptom Rating Scale (GSRS) and Psychological General Well-Being (PGWB) Index questionnaires. Results The duration of the IBS symptoms was a mean of 10 years (range 3–25). Symptoms were present, according to the scores of the GSRS and the PGWB index, at the time the patients underwent the CE. In the majority, 24 of 27 IBS patients examined, no specific small intestinal lesions were seen on CE. In two patients, CE revealed multiple small intestinal lesions such as ulcerations and/or erosions, and in one patient a duodenal ulceration. Conclusion In the vast majority of patients who fulfil the symptom criteria of IBS, no pathological mucosal lesions can be found by CE explaining the symptomatology. However, a subgroup of these patients may benefit from investigation by CE to reconsider the diagnosis.