Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most widely used medications. However, NSAID intake is accompanied by an increased risk of gastroduodenal side effects. These adverse events are largely attributed to the ability of these drugs to suppress prostaglandin synthesis, penetrate the mucosal layer in the acid media of the stomach and damage epithelial cells. However, it is becoming clear that such mediators as prostaglandins, NO and lipoxins can protect the stomach from injury. This injury can largely be prevented through suppression of gastric acid secretion (mainly with proton pump inhibitors). In contrast, the pathogenesis of intestinal injury induced by NSAIDs is less well understood. There is no evidence that suppression of gastric acid secretion will reduce the incidence or severity of NSAID enteropathy. In this review the results of recent studies are described, which will help to clarify some mechanisms of development of NSAID gastropathies and NSAID enteropathies and to improve the treatment of these patients.