Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of hepatic pathologies ranging from simple steatosis (SS) to hepatocellular carcinoma. Intestinal microbiota (IM) is composed of trillions of microorganisms existing in the gut. It has 150 times more genes than the host. Changes in the composition and function of the IM are associated with different diseases, including NAFLD. In this condition, IM could have a pathogenic role through different mechanisms such as energy salvaging from food, an inflammatory stimulus, a modulation of the innate immune system, regulation of bile acid turnover, alteration of choline metabolism and increasing endogenous ethanol levels. This review is an update on the role of the intestinal microbiota in NAFLD and the possible mechanisms involved.