Background: Score models to predict endoscopic diagnosis in dyspepsia may compensate for the unreliable clinical diagnosis. This study aimed to construct and test score models designed to predict diagnosis in dyspeptic patients managed in primary care. Methods: Three models to predict organic dyspepsia, major dyspepsia, or peptic ulcer were constructed by regression analysis of clinical data from 1026 consecutive dyspeptic patients referred for endoscopy. The models were tested in 207 patients in primary care, who were potential candidates for endoscopy. Validation experiments were analysed using receiver operating characteristic (ROC) curves. Results: Significant losses of predictive power were found for all models when applied to primary care patients, and no model could be used as a reliable decision support instrument in primary care. Conclusions: Predictive score models developed in patients referred for endoscopy are not reliable when applied to patients in primary care who are potential candidates for endoscopy. Future models should be constructed and validated in unselected primary care populations.