The incidence of non-alcoholic fatty liver disease (NAFLD) and its related conditions including obesity and metabolic syndrome has dramatically increased in Western countries. Gut microbiota contributes to body weight regulation and related disorders like NAFLD by influencing metabolic and immune host functions. High fat diet may induce small intestinal bacterial overgrowth (SIBO) and dysbiosis which determine a malfunction of tight junctions (TJ) playing a critical role in the increase of intestinal permeability and the translocation of bacteria and their products. The endotoxaemia induces an inflammatory response that determines the development of insulin resistance, body weight gain, lipogenesis, fibrogenesis and hepatic oxidative stress which contributes to the second hit mechanisms in the pathophysiology of non-alcoholic steatohepatitis. In these categories of predisposed patients these mechanisms may be exacerbated by the administration of non-steroidal anti-inflammatory drugs (NSAIDs) that causes an initial alteration of intestinal permeability up to more serious complications. NSAIDs enteropathy is due to enterohepatic recycling of drug resulting in a prolonged and repeated exposure of the intestinal mucosa to the compound and its metabolites leading to so called topical effects. The pathogenesis of NSAID enteropathy is less linked to their ability to suppress cyclooxygenase activity and to the presence of gastric acid, even if more and more emphasis is placed on co-administration of antisecretory agents which determine hypocloridia, associated with small intestinal bacterial overgrowth and bile acid dysmetabolism, responsible of exacerbation of NSAID-induced intestinal damage. Prevention and treatment of NSAID enteropathy and his systemic complication like NAFLD have become major priorities, consequently novel approaches directed toward other pathomechanisms and research of new therapeutic strategies are needed.