Helicobacter pylori has been classified as a human carcinogen contributing to the pathogenesis of gastric cancer. Extensive sero-epidemiological studies and recently animal experiments have established a close link between H. pylori infection and the development of gastric cancer. However, the molecular changes induced by H. pylori directly or the concomitant chronic inflammation of the gastric mucosa, and the impact of these changes on the subsequent development of gastric cancer, remain largely unknown. This review will highlight the present knowledge on the molecular pathogenesis of gastric cancer with an emphasis on molecular and genetic alterations which develop due to chronic infection of the gastric mucosa by H. pylori.