GPs face a potential dilemma in deciding which test to use for detection of Helicobacter pylori. For patients with dyspepsia, the National Institute for Health and Clinical Excellence (NICE) advises primary care practitioners to adopt a 'test and treat' policy before considering a referral for gastroscopy. There are many ways of testing: serology, urea breath test, and faecal antigen test. NICE does not advocate any preferred single test for detecting H. pylori. In the current study a multi-stakeholder 2-day workshop was established to agree and populate a cost-effectiveness decision analysis model. The aim was to analyse the three types of tests available for H. pylori and to determine which is the most practical and cost effective. Agreement on the costs and diagnostic values to be entered into the decision-analytic model was achieved. Results indicate that the faecal antigen test was the most effective in terms of true outcomes and cost. One thousand virtual patients were allocated to each of the three tests. Serology had 903, urea breath test had 961, and the faecal antigen test had 968 true positive outcomes. Data indicate that the faecal antigen test is the preferable strategy for diagnosis of H. pylori in primary care. This has implications for implementing new testing processes and for commissioning new diagnostic pathways for use in primary care.