Background: Gastro-oesophageal reflux disease (GERD) and dyspepsia affect 25-40% of the general population. In the absence of alarm symptoms, the current recommended policy in young dyspeptic patients is a 'test and treat' strategy for Helicobacter pylori; in GERD patients, a therapeutic trial with proton pump inhibitors is the treatment of choice. Aim: To create a short and simple clinical algorithm, for the diagnosis and treatment of patients with upper gastrointestinal complaints. Methods: The clinical usefulness and cost-effectiveness of the new algorithm were evaluated in a controlled clinical trial, held in primary-care clinics in Israel. Clinical and economical treatment outcomes were evaluated after 1, 3 and 6 months comparing doctors who used the algorithm (cases) vs. those who did not (controls). Results: 78 cases and 54 controls completed the 6 months of follow up. The improvement in symptom severity and quality of life was greater in the cases than in the controls (P < 0.05). General practitioner clinics visits (P = 0.04), gastroenterology clinics visits (P = 0.02) and medication costs (P = 0.004) were all significantly reduced among cases. Controls underwent also more imaging tests (computerized tomography, ultrasound and X-ray) and endoscopies. The average cost for 6 months' treatment and follow-up was $US 199 for cases compared with an average of $US 336 in the control group. Conclusion: The use of a clinical decision-support tool can facilitate and promote the implementation of management guidelines by general practitioners. The short algorithm presented in the study was found to be useful and easy to apply in clinical practice. Its effectiveness can be further increased by implementing it in computerized medical systems.