Gastrointestinal disorders are common in the general population, with annual prevalence figures ranging from 20% for irritable bowel syndrome to over 40% for dyspepsia. Less than one-third of patients consult general practitioners for these problems, and anxiety about serious disease and cancer are as important in the decision to consult as symptom severity. Gastrointestinal disorders have significant socioeconomic effects in the community, and account for 10% of the work of general practitioners in the UK. The health economics implications of management in primary care relate principally to the costs of investigation and therapy, notably antisecretory drugs, endoscopy, radiology and specialist referral. Although guidelines based on evidence and agreed between primary and secondary care physicians offer an attractive approach to rationalizing the use of resources, there is at present little health service research evidence on which to base important decisions. For example, in dyspepsia, the role of Helicobacter pylori identification and eradication in an overall management strategy in primary care has yet to be defined. An exploration of the clinical economics of gastrointestinal disorders in general practice raises a number of research questions, which will require the attention of both generalists and specialists.