Objective To prospectively assess the accuracy of a scoring system to predict organic diseases in dyspeptic patients in an area of South Europe, and to compare it with that of Helicobacter pylori testing in patients with dyspepsia in an environment with high prevalence of H. pylori infection. Methods Symptoms and demographic data were recorded in 501 consecutive dyspeptic patients referred to an outpatient gastroenterology clinic. A simple scoring system was constructed from the predictive factors obtained in a multi‐variate logistic regression analysis. Overall predictive accuracy was assessed with the c statistic. The model was validated using bootstrap techniques. The accuracy of clinical judgement and H. pylori testing to predict endoscopic diagnosis was also assessed. Results Organic dyspepsia (peptic ulcer, oesophagitis or malignancies) was diagnosed in 45% of the patients. The test for H. pylori was positive in 68%, and 29% of infected patients had an ulcer. The organic dyspepsia predictive model had an accuracy of 0.79, which decreased to 0.77 after validation adjustment. The predictive accuracies for clinical judgement and H. pylori testing were 0.69 and 0.61, respectively. The addition of H. pylori testing to the scoring system resulted in a minor improvement of the predictive accuracy. Conclusion In an environment with a high rate of H. pylori infection and a low prevalence of peptic ulcer among infected patients, a scoring system has higher predictive accuracy for the diagnosis of organic disease than H. pylori testing. Moreover, in this setting, H. pylori testing adds a minimum value to the predictive capability of the scoring system.