BACKGROUND: Previous studies have failed to identify manometric patterns of gastrointestinal motor activity that can distinguish dyspepsia from health. AIMS: To test the hypothesis that the combined use of prolonged, ambulatory, antrojejunal manometry and computer aided analysis in patients selected for the severity of their symptoms could reveal new insights into gastrointestinal motor activity in patients with severe motility-like dyspesia. METHODS: Twenty four hour antrojejunal ambulatory manometry was performed in 14 patients and 10 healthy volunteers. Parameters characterising digestive and fasted motility were obtained by a validated computer program and visual analysis. Scoring systems quantified the degree of dysmotility as well as the severity of symptoms. Gastric emptying times were measured in each patient. RESULTS: There was a high prevalence of antral and jejunal dysmotility both during the interdigestive period (71% of patients) and in the postprandial period (78%). During the interdigestive period there was a reduced incidence of antral and jejunal phases, a larger contribution of phase 2 during migrating motor complex cycles, and aberrant configuration of jejunal phase 3 in 29% of patients. Postprandially, the most frequent finding was antral (29% of patients) or jejunal (29%) hypomotility or hypermotility. Minute rhythm was present both during the postprandial (29% of patients) and the interdigestive period (21%). There was no positive correlation between symptom scores, gastric half emptying times, or motility scores. CONCLUSION: Even with the use of prolonged recordings and advanced computer aided analysis, it is not possible to identify a specific motor pattern which can discriminate patients with severe motility-like dyspepsia from those with other diseases or even healthy individuals. Clinical symptoms or gastric half emptying times are poor predictors of gastrointestinal dysmotility in patients with functional dyspepsia.