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Helicobacter pylori-associated gastritis may progress or be complicated by peptic ulcer and gastric malignancy, including gastric carcinoma and mucosa-associated lymphoid tissue lymphoma. Predicting who develops malignancy remains a clinical challenge. The molecular understanding of pathways that are associated with progression of the normal gastric epithelium to malignancy together with classic histologic parameters are promising ways of tackling this problem. Ideally, molecular tools used for screening should be available as noninvasive tests, such as examination of markers detectable in blood samples, but these are not currently available. In contrast, molecular markers that correlate with cancer risk can be examined in the epithelium after endoscopic biopsy and can be of importance in identifying individuals at risk, especially if combined with other parameters of gastric cancer risk.